On the library file management page, an assembly can be added by choosing Add assembly… from the Assembly drop-down list (Figure 1). If the list is long, you may need to scroll to the bottom.

In the Add assembly dialog, choose the Species from the drop-down list (Figure 2), followed by the Assembly version (Figure 3) and click Add. The dialog will automatically load commonly used assembly versions for the selected species (Figure 3). If the assembly version you want does not appear in the list, choose Other and type the custom assembly version name (Figure 4). Characters such as $ * | \ : " < > ? / % cannot be used in custom names. Note that If an assembly version for a given species already exists on your system, it will not appear in the drop down list.

If the species you want to add does not appear in the list, scroll to the bottom of the species list, choose Other and manually type the species name and assembly version (Figure 5).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

To modify the settings, click your avatar at the top right corner of the home screen and select Settings (Figure 1). The left side of the page will display the different settings that can be customized:

Figure 1. Accessing the Settings page

Additional Assistance

Can’t remember your login information? To recover your account, select Can’t access your account in the Login page (Figure 9). Note that this feature may not be functional if your IT administrator set restrictions for emails sent from your Partek Flow server.

Figure 1. Recovering forgotten account information

This will take you to a menu that lets you recover your password once you enter your username (Figure 10).

Figure 2. Recovering forgotten password

On the other hand, if you have forgotten your username, select I don’t remember my username and enter the email address associated with the user account (Figure 11).

Figure 3. Recovering forgotten username

An email will be sent to the address with the username information.

Additional Assistance

Partek Flow allows an administrator to configure the system through the Settings menu. This section will describe the following sections:

Aside from System information, these sections can only be viewed using a Partek Flow administrator account.

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Partek Flow enables certain components of the software to be configured, such as hiding/showing special tasks and managing saved task parameters like option sets.

This section will illustrate how to use the following options:

• Filter Management

• Library File Management

• Option Set Management

• Task Management

• Pipeline managment

• Lists

Note that the Task management page will only be accessible using a Partek Flow administrator account.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow user accounts can be tied to an organization’s Lightweight Directory Access Protocol (LDAP) database. These can be configured by administrator accounts using the LDAP Configuration menu (Figure 1). Click on the icon to edit the LDAP configuration. Enter the settings relevant to your domain. Consult with your organization’s LDAP database administrator for assistance with configurations. For more information about any of the fields, mouse over the .

Once the LDAP settings have been successfully configured, proceed to the User management section of the Settings page then click on . The Source field should denote the name of the LDAP configuration entered. Typing a few characters of the username will prompt Partek Flow to suggest users that are available in your LDAP database to add.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Profile options are controlled via the Personal Settings section of the Settings page (Figure 1).

Figure 1. Personal settings section of the Settings page

My profile contains basic user information. If no avatar picture is provided, a silhouette is displayed by default (Figure 2).

Figure 2. My profile page with basic user information

The display name, e-mail address and password can be changed by selecting the Edit details button and then providing new information (Figure 3). Note that you may not have permission to change some of these details if restricted by your IT administrator. Consult with your IT department regarding this configuration.

Figure 3. Editing user details

When changing a password (or creating a new one) the length of the password is evaluated and will be classified as either Too weak, Good, or Strong (Figure 4). Passwords that are deemed too weak will not be accepted.

Figure 4. Password is evaluated upon creation

To change your avatar, select the Change image button. You can select from one of the available avatars (Figure 5), or you can upload a custom avatar. Acceptable file formats are .png, .gif, .jpg., and .jpeg.

Figure 5. Change image dialog

For Partek Flow licenses that include the enterprise feature of User Disk Quotas, a disk usage row appears on the profile of each user (Figure 6).

Figure 6. User Profile showing disk usage and quota

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow enables each user to customize her/his own settings, including the avatar, e-mail address, and time zone.

This section will illustrate how to use the following options:

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Click the + Add reference files button under the and choose Cytoband from the Library type drop-down list in the Add reference sequence dialog (Figure 1). If a reference sequence is already associated with an assembly, Cytoband will be the only option available in the Add reference sequence dialog and will not appear in a drop-down list (Figure 1).

If you are using a custom assembly (e.g. for a non-model organism), the Download cytoband option will not be available (Figure 2).

Additional Assistance

The System information page can be found in Settings>System information (Figure 1).

For new users, Partek Flow provides sample RNA-Seq data available for download. To download the files, select the corresponding data set under Download tutorial data. Depending on the dataset you select, this will automatically create a new project either called Brain vs UHR or iDEA Challenge.

After the data has finished downloading, the samples will automatically be imported into the project. See our for more information.

Partek Flow details displays the build version currently installed in your server as well as your Root and Library directories, the architecture version and the internet browser you are currently using.

Server details lists additional information about the server that Partek Flow is installed in. Java details lists the version of Java and its configuration as used by Partek Flow. On the other hand, Partek Flow license details lists the licenses available for use in your Partek Flow server.

Figure 1. System information page when viewed by a regular user

Additional Assistance

The library file management tool in Partek Flow provides an easy way to create, process and manage reference sequences, cytoband files, annotation models, aligner indexes, gene sets, variant databases and microarray probe sequence files.

For a quick start, please watch the short videos below:

Quickly setup library files for the hg19 human reference genome assembly.

https://github.com/illumina-swi/partek-docs/assets/167460925/f43089e7-e02e-4f0c-93ad-14dca4130435

The process can be adapted to the different kinds of file types.

Adding library files for a non-model organism

https://github.com/illumina-swi/partek-docs/assets/167460925/f6a17ed6-793e-4d86-b58f-63b82a111864

You can watch the full webinar on our website.

This user guide will cover the following topics:

• Library File Management Settings

• Library File Management Page

• Selecting an Assembly

• Library Files

• Update Library Index

• Creating an Assembly on the Library File Management Page

• Adding Library Files on the Library File Management Page

• Adding a Reference Sequence

• Adding a Cytoband

• Adding Reference Aligner Indexes

• Adding a Gene Set

• Adding a Variant Annotation Database

• Adding a SnpEff Variant Database

• Adding a Variant Effect Predictor (VEP) Database

• Adding an Annotation Model

• Adding Aligner Indexes Based on an Annotation Model

• Adding Library Files from Within a Project

• Microarray Library Files

• Adding Prep kit

• Removing Library Files

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Choosing an Assembly from the drop-down list at the top will display the associated library files in the panel below. Assemblies are named by the species and the build version (e.g. Homo sapiens (human) - hg19). Different build versions for the same species are regarded as separate assemblies (Figure 1). Administrative users can delete a selected assembly by clicking the bin () icon.

Additional Assistance

The results of differential gene expression analyses (GSA or ANOVA) in Partek Flow can be filtered to extract meaningful results, e.g. statistically significant genes. User-defined filters can be saved and applied to other projects.

This user guide will cover the following topics:

Saving a Custom Filter

On a Feature list task report, specify the criteria to filter the table of statistical results using the Filter dialog (Figure 1) and click the Save filter button.

Name the filter by typing into the Filter name box in the Save filter dialog and click the Save button (Figure 2).

Saved filters will appear in the Saved filters section in the Filter dialog (Figure 3). Saved filters are only available to the Partek Flow user that created them. They will not be available to other administrative or non-administrative users on the same Partek Flow instance.

To apply a saved filter to a table of statistical results, click the filter name in the saved filters section in the Filter dialog. If a filter is applied to a table, the filter name will appear at the top of the Filter dialog.

Filter Management Page

From the action list, select View filter details to show the filter details (Figure 6). To delete a filter, click the Delete filter button (Figure 5)

Additional Assistance

The library files associated with the selected assembly are organized into several sections. Below is some information on each section.

• Reference Files

• Reference aligner indexes

• Gene sets

• Variant annotations

• SnpEff variant databases

• VEP database

• Annotation models

• References

Reference Files

This section includes two types of library file: reference sequence and cytoband files.

Reference sequences are the chromosome/scaffold/contig DNA sequences for a species. A reference sequence file is typically in FASTA or 2bit format. The reference sequence of a species is used for aligner index creation, variant detection and visualization of the reference sequence in the Chromosome view.

Cytoband files are used for drawing ideograms of chromosomes in the Chromosome view, including positions of cytogenetic bands if known.

Reference aligner indexes

Next-generation sequencing aligners require the reference sequence to be indexed prior to alignment, as this greatly increases alignment speed. An index consists of a set of files (Figure 1) and are generally aligner specific. For example, if you wish to align using BWA, you need a BWA index.

Some of the supported aligners share indexes. If you want to align using Tophat, the Bowtie aligner indexes can be used. If you want to align using Tophat2, the Bowtie2 aligner indexes can be used.

Some aligner indexes are version specific, so care must be taken if you change aligner versions. For example, the index files for STAR version 2.4.1d are different to older versions of STAR.

This section contains aligner indexes for aligning to the whole genome. If you wish to align to a subset of the genome, e.g. targeted amplicons or the transcriptome, you must generate these indexes in the Annotation models section.

Gene sets

Gene set files are required for biological interpretation analyses (e.g. GO enrichment). Genes are grouped together according to their biological function. Gene set files have to be in GMT format, where each row represents one gene set. The first column of a GMT file is the GO ID or gene set name. The second column is an optional text description. Subsequent columns are the gene symbols that belong to each gene set. Gene ontologies for various model organisms are available for automatic download from the Partek repository (source: geneontology.org). Because gene ontologies are frequently updated, geneontology.org is checked for updates quarterly. You can check for recent updates to the Partek repository here.

Variant annotations

Variant annotation databases are collections of known genomic variants (e.g. single nucleotide polymorphisms). If you have performed a variant detection study, detected variants can be searched against variant annotation library files to see if the detected variants are known from previous studies. Furthermore, you can validate detected variants against 'gold-standard' variant annotation library files. Variant annotation files are typically in VCF format.

Variant annotation databases from commonly used sources (e.g. dbSNP) are available for automatic download from the Partek repository. Because variant annotation databases are frequently updated, these sources are checked for updates quarterly. You can check for recent updates to the Partek repository here.

SnpEff variant databases

SnpEff1 is a variant annotation and effect prediction tool that requires its own variant annotation files, separate to the other Variant annotation library files. If you wish to use SnpEff, library files need to be added to this section.

VEP database

The Ensembl Variant Effect Predictor (VEP) is another variant annotation and prediction tool that requires its own annotation files, separate to the Variant annotation library files. If you wish to use VEP, library files need to be added to this section.

Annotation models

This section includes two types of library file: annotation models & aligner indexes.

Annotation models describe genomic features (e.g. genes, transcripts, microRNAs) for a specific version of the reference sequence. Annotation models contain labels (e.g. gene ID) and genomic coordinates (e.g. chromosome, start & stop position) for each feature.

Annotation models will appear in separate tables (Figure 2). If you have multiple versions of annotation models from the same source, it is advisable to distinguish them by their date or version number.

Annotation models from commonly used sources (e.g. Refseq, ENSEMBL) are available for automatic download from the Partek repository. Because annotation models are frequently updated, these sources are checked for updates quarterly. You can check for recent updates to the Partek repository here.

Annotation models are used for quantification in gene expression analyses, annotating detected variants (e.g. to predict amino acid changes), visualizations in Chromosome view, generating coverage reports and for aligner index creation (see Adding Aligner Indexes Based on an Annotation Model). Typical file formats include GTF, GFF, GFF3 and BED.

The aligner indexes in the Annotation models section are required if you wish to align to a subset of the genome as defined by the annotation model, e.g. target amplicons or the transcriptome. The reference sequence is still required to generate an aligner index for an annotation model. As with whole genome alignment, indexes are aligner specific, although some aligners share indexes and are version specific (see Reference aligner indexes). The aligner indexes generated will be added to the corresponding annotation model table (Figure 2).

References

1. Cingolani P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 6(2):80-92. PMID: 2272867

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

The user’s general preferences, email notification, projects, graphics preferences, library file and list sharing, and analysis tab options are listed on the My preferences page (Figure 1).

Figure 1. My preferences page with default settings

The default values can be changed through the Edit user preferences button at the bottom of the page (Figure 2).

Figure 2. Editing My preferences information (an example is shown)

Click Save at the bottom of the page to retain any changes made to My preferences.

Additional Assistance

To access the library file management page click the avatar in the top right corner and choose Settings. Then under Components on the left, click Library files.

The library files page has three tabs - Genomic library files, Prep kits files, and Other library files. This section of the user guide will focus on the Genomic library files tab, which is relevant for next-generation sequencing analysis (Figure 1).

The arrows ( v / ) expand/collapse each section. Associated library files are shown in a table in each section. In the Actions column of each table, the View library file details button displays additional library file details, the bin () icon dissociates a library file. The hourglass () icon indicates a library file is being created.

Additional Assistance

Click the + Add gene set databases button under the Gene set databases section header on the .

If you are using an assembly supported by Partek (e.g. human), a gene set from will appear in the Gene set database drop-down list (Figure 1). Select the Download gene set database radio button and click Create.

If you prefer to add a custom gene set, or if you are working with a custom assembly, choose Add gene set database from the Gene set database drop-down list (Figure 2). Name the gene set by typing into the Custom Name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. A gene set file can be added from the Partek Flow Server or a URL download link. The behavior of each option is similar to when importing a reference sequence (see ). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gmt and various compressed formats).

Additional Assistance

The System preferences menu accessible to administrator accounts (Figure 1) allows you to configure Partek Flow preferences. These preferences generally govern the activities of other users within the Partek Flow server. They can only be viewed and configured by Administrator accounts. The preferences are subdivided into the following sections:

• [General preferences](#general preferences)

Modifying preferences under the User quotas and limitations section require the User Disk Quotas license. Upon opening the system, all sections are collapsed except for Filesystem and storage (Figure 1).

Figure 1. System Preferences Page

Filesystem and storage

Data download directory

• Specifies the directory on the server to which the data files will be uploaded

Library file directory

• Specifies the directory on the server to which the library files will be uploaded

Default project output directory

• If Sample file directory is selected, files will be written on the same directory in which the sample files are located

• If Other is selected, a directory on the server must be specified to which the project output files will be written

• The user can override this setting by specifying the output directory in the project’s Data tab after at least one sample has been created

• If Enforced private directory is selected, files will be written on the user's private directory. The alternative folder specified after else will be used if no private directory is assigned to a user.

Store file-path symbolic links

• If Yes is selected, Partek Flow will store new file paths with any symbolic links intact, making it easier to change where the links point. Otherwise, new paths are stored with symbolic links replaced by the directories to which they point, guaranteeing that Partek flow can uniquely identify each file and recognize when it already has information about that file. Changing the setting does not affect file paths already stored or the ability of Partek Flow to locate earlier files

Activity log retention

• Number of months activity logs are kept for

Task queue and job processing

Figure 2. Editing the Task queue and job processing preferences

Start Internal worker at Partek Flow server startup

• When enabled, an internal worker will be started upon server restart

Maximum running projects

• Sets the maximum number of projects that will run simultaneously. Any tasks already running will be completed before this takes into effect

Adjust job nice value

• Niceness value that is added to Partek Flow commands. Higher values are nicer. Set to 0 to disable

Show anonymous tasks on the queued tasks page

• If Yes is selected, all users can view the tasks queued up on the server and tasks that are not shared with the user will appear as anonymous

Show warning when no workers are connected

• If Yes is selected, a warning will be displayed when no workers are attached to the Partek Flow server

Email admins long running queued task

• If Yes is selected, Partek Flow will email admins (Figure 3) if a running task has a remaining runtime longer than the specified days and adding more workers could speed up the task

Figure 3. Example of an email sent to Partek Flow administrators for predicted long runtimes

User quotas and limitations

Figure 4. Editing User quotas and limitations preferences

Only administrators can manage library files

• If Yes is selected, only administrators can import and delete library files and regular users can only view library files

Only administrators can create system-wide attributes

• If Yes is selected, only administrators can create system-wide attributes within projects

Upload file size limit

• Size limit for files that can be uploaded using the My computer option

• Setting this to 0 removes file size limit

• Sets the default size of disk quota available for all users

• Disk quotas for specific users can be set in the User management page

• If Set as the quota for users having none is checked, disk quotas are retroactively set for all users currently without disk quotas

• Selecting None means there are no disk quotas across all users

• Specifies the actions when user reaches 80% of their disk quota

• An email can be sent to the user and/or the administrators (Figure 5)

• The user can also be prevented from importing additional samples and running tasks until they clear additional space

Figure 5. Example of an email sent to Partek Flow administrators about user quota

• Specifies the actions when user reaches their disk quota

• An email can be sent to the user and/or the administrators (similar to Figure 5)

• The user can also be prevented from importing additional samples and running tasks until they clear additional space

Authentication settings

Figure 6. Configuring Authentication settings

Days for user to set password

• If a user requests a password reset, this specifies amount of time the user has to reset their password

Use proxy server

• Allows administrator to configure proxy settings for the Partek Flow server

• Note that port number changes require a corresponding update to tomcat/conf/server.xml and a Partek Flow server restart

Allow users to override the default session timeout

• If checked, this gives each user the ability to override the default session timeout with their own settings as specified in "My preferences"

Default session timeout

• The amount of time, in minutes, before users are automatically logged out

• This protects users in the event that they walk away from their computer

Require HTTPS for all pages

• If checked, this requires HTTPS to load Partek Flow pages. Specify HTTPS port

Email settings

These settings allow Administrators to use the embedded email server within Partek Flow. Select the checkbox to configure mail server (Figure 7).

Figure 7. Configuring Email settings

Email users on transfer of project ownership

• Administrators can configure whether email notifications are sent when project ownership is transferred. By selecting the relevant checkbox, the new or previous project owner can be notified.

Extra text to email to new users

• If the Email users on creation checkbox is selected, new Partek Flow users will receive an email with a link to set their password within Partek Flow. The email will include this extra text, which may have URLs in it. This setting does not affect user accounts that come from LDAP, because these accounts use the password stored in LDAP, not in Partek Flow

General preferences

Figure 8. Editing General preferences

Data table decimal precision

• Specifies the number of decimal places displayed

Additional Assistance

Note that this task is for adding indexes for alignment to the whole genome. If you want to align to the transcriptome or another set of genomic features, see Adding Aligner Indexes Based on an Annotation Model.

Click the + Add reference aligner indexes button under the Reference aligner indexes section header on the library file management page. Choose the aligner index you wish to add from the drop-down list in the Add aligner index dialog (Figure 1). The following indexes can be added:

• Bowtie

• Bowtie 2

• HISAT 2

• TMAP

• BWA

• GSNAP

• GSNAP v8

• STAR

• STAR 2.5.3a

• STAR 2.7.3a

• STAR 2.7.8a

• Issac 2

• RSEM

• Salmon

• Cell Ranger ARC 2.0.0 reference

• Minimap2

If you are using an assembly supported by Partek (e.g. human), there are three radio button options: Download index; Build index or Import index (Figure 1). Certain aligner indexes may not be available for automatic download because the file sizes are too large to download efficiently.

If available, select Download index and click Create to get the chosen reference aligner index from the Partek repository.

Alternatively, select Build index and click Create to build the reference aligner index. To build an aligner index, a reference sequence file must already be associated with the assembly. Depending on the aligner, you may have to specify further parameters. Consult the user documentation for each aligner for guidance (usually available on-line).

Alternatively, select Import index and click Create to add an aligner index from another source. An aligner index can be added from the Partek Flow Server or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a Reference Sequence). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible. This will vary for each aligner.

For custom assemblies (e.g. for non-model organisms), only the Build index and Import index options are available (Figure 2).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

To review and edit library file management settings, you must be logged into Partek Flow as a user with administrator privileges. Click on the avatar in the top right corner and choose Settings. Then click System preferences on the left.

You can review the current library file directory location (Figure 1).

To change where the library files are stored, click Edit filesystem and storage and click Browse () icon to point to another directory (Figure 2).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Click the + Add variant annotations button under the Variant annotations section header on the library file management page.

If you are using a human - hg19 assembly, variant annotation databases from various sources will appear in the Variant annotation drop-down list (Figure 1). Available variant annotation database sources include:

• dbSNP

• Kaviar

• NHLBI Variant Server

• 1000 Genomes

Multiple versions of the above databases are available. For human - hg38, only dbSNP is currently available. This list is periodically updated.

Choose a database from the drop-down list, select the Download variant database radio button and click Create.

If you prefer to add a custom variant annotation database, perhaps from another source or 'gold-standard' validated variants, choose Add variant database from the Variant annotation drop-down list (Figure 2). Name the variant annotation database by typing into the Custom Name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. A variant annotation database can be added from the Partek Flow Server or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a Reference Sequence). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.vcf and various compressed formats).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

The library index is a file that contains download sources for all Partek distributed library files. An automatic update of this file will occur every 24 hours (Figure 1), so this normally doesn't require any attention. If you do wish to manually update the library index, click Update Library Index at the bottom of the Library file management page.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Library files can be added to an assembly by clicking the + Add reference files button under the Reference files section (Figure 1) on the library file management page. If all possible library files are already associated in the section, the Add reference files button will be disabled (Figure 1).

Clicking + Add reference files button opens a dialog specific to the section. Choose a library type from the drop-down list in the Add reference sequence dialog (Figure 2) and the dialog will present options specific for each type. If certain library files have already been associated with an assembly, they will not appear as options in the dialog. For example, if a reference sequence has already been associated with an assembly, it will not appear as an option in the drop-down list shown in Figure 2.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Click the + Add SnpEFF variant databases button under the SnpEff variant databases section header on the library file management page.

If you are using human (hg19 and hg38), mouse (mm10) or rat (rn5 and rn6) assemblies, various versions of SnpEff variant databases are available for automatic download (Figure 1).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Note that this task is for adding indexes for alignment to a subset of the genome (e.g. the transcriptome). If you want to align to the whole genome, see Adding Reference Aligner Indexes.

On the library file management page, click the + Add annotation models button at the Annotation models section and choose Aligner index from the Library type drop-down list in the dialog (Figure 1).

Choose the aligner you wish to use from the Aligner drop-down list (Figure 1). All aligners are available for indexing to an annotation model.

The annotation model(s) that have already been associated with an assembly will appear at the top of the Index to drop-down list. Choose the annotation model you wish to index to, select the Build index radio button and click Create (Figure 1). To build an aligner index based on an annotation model, a reference sequence file must already be associated with the assembly.

If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources will appear in the Index to drop-down list in addition to the ones that have already been associated with the assembly. If you choose an annotation model that has not already been associated, it will automatically be downloaded prior to building the index.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

On the , click the + Add annotation models button in the Annotation models section, choose Gene/feature annotation from the Library type drop-down list in the dialog (Figure 1).

If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources (e.g. ENSEMBL, GENCODE) will appear in the Annotation model drop-down list in the dialog. Choose an annotation model, select the Download annotation file radio button and click Create (Figure 1).

If you prefer to add a custom annotation file or if you are working with a custom assembly, choose Add annotation model from the Annotation model drop-down list (Figure 2). You may need to scroll to the bottom of the drop-down list to see this option. Name the annotation model by typing into the Custom name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names.

Select the source of annotation file and click Next. If the annotation file format is gtf, gff, gff3 or bed, a preview of the first 10 rows of the file will be shown on the screen (Figure 3). You must then specify the type of annotation file by choosing an option from the Annotation type drop-down list (Figure 3). Choose mRNA for whole transcriptome annotations, where both gene and transcript level information are present. Choose microRNA for precursor or mature microRNA transcript annotations. Choose Amplicon for targeted amplicon sequencing annotations. Choose Other for annotation files that do not fall into the other four categories (e.g. lncRNA).

For text annotations with both gene- and transcript-level information select mRNA from the drop-down menu. You can manually specify which column corresponds to the Transcript ID or Gene ID by selecting the corresponding radio button next to the column with that information (Figure 4).

Genome coordinates for annotation models stored in Partek Flow are 1-based, start-inclusive, and stop-exclusive. This means that the first base position starts from one, the start coordinate for a feature is included in the feature and the stop/end coordinate is not included in the feature. These are the genome coordinates that are printed in various task reports and output files when an annotation model is involved in the task. When custom annotation files are added to Partek Flow, the genome coordinates are converted into this format. The coordinates are converted back if necessary for a specific task. Figure 5 shows how the genome coordinates vary between different annotation formats.

Additional Assistance

Click the + Add VEP database button under the VEP database section on the library file management page.

If you are using an species supported by Partek (i.e., human, mouse, rat), a VEP database from ENSEMBL will be available for automatic download. Select the Download database radio button and click Create (Figure 1).

If you are working with a custom assembly, choose the Import database radio button and click Create (Figure 2). A VEP database can be added from the Partek Flow Server or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a Reference Sequence). ENSEMBL maintains an extensive list of VEP databases for various species. We recommend going to ENSEMBL's ftp download site and finding the VEP database download link for your species of interest.

One VEP database is allowed per genome assembly. Once a VEP is successfully imported, the + Add VEP database button will not be shown (Figure 3).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Missing library files can be added when setting up tasks within a project, without having to navigate to the library file management page. The user interface will vary depending on the task and which library files already exist on your system. Below are two examples scenarios.

Adding a missing whole genome aligner index (Bowtie 2 in this example)

1. Under the Analyses tab of a project, select an Unaligned reads data node

2. From the context sensitive menu on the right, choose Aligners followed by Bowtie 2. On the alignment task setup page, Partek Flow will display all assemblies that have a Bowtie 2 index (whole genome and transcriptome) in the Assembly drop-down list. If the assembly you want is missing, choose New assembly… from the drop-down list (Figure 1)

1. Choose the species and assembly in the Add Bowtie 2 index dialog. If the species and assembly you want do not appear in the drop-down lists, choose New species... and manually type the names (Figure 2)

2. Choose Whole genome from the Index drop-down list (Figure 2)

3. Select the Build index radio button (Figure 2)

4. Click Create (Figure 2)

Once the new Bowtie 2 index has been specified, you are able to queue the alignment task and it will execute once the Bowtie 2 index has been built.

Add a missing gene set file for enrichment analysis

1. Under the Analyses tab of a project, select a Feature list data node

2. Choose Biological interpretation from the menu on the right, followed by Gene set enrichment

3. Select Gene set database radio button for Database. If the species and assembly you want do not appear in the Assembly drop-down list, select New assembly... (Figure 3)

1. If you are working with an assembly/species supported by Partek (e.g. human), choose a gene set from the Gene set database drop-down list (Figure 4), select the Download gene set database radio button and select Create. Alternatively, choose Add gene set database from the Gene set database drop-down list, manually type the custom gene set name and click Create to import your own gene set from the Partek Flow server or URL (Figure 5). Characters such as $ * | \ : " < > ? / % cannot be used in custom names. If you are working with a custom species/assembly (e.g. for a non-model organism), only the Add gene ontology source option is available.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Microarray library files can be managed under Microarray library files section on Other library files tab on the Library file management page (Figure 1). The chip name and download source of stored Microarray library files will be shown in the table in this section. For more information, refer to the section.

Microarray probe tab files are used for processing microarray data in Partek Flow. When microarray intensity data files (e.g. Affymetrix .CEL files) are imported into a project, the chip type is automatically detected and the appropriate probe tab annotation file is downloaded. Thus, you would normally not need to manually add any probe tab annotation files.

To add a (e.g. for a custom chip), click the + Add probe sequence button at the Microarray library files section (Figure 1). Scroll to the bottom of the Chip name drop-down list and choose Other / Custom. Name the chip by typing into the Custom name box and click the Create button (Figure 2). Characters such as $ * | \ : " < > ? / % cannot be used in custom names.

Additional Assistance

Partek distributes prep kit files for a variety of single cell technologies, such as 10x Genomics, Drop-seq, and Fluidigm C1. Prep kit files are required to process single cell fastq files. If you need to add a new prep kit in order to process your fastq files, you will need to get detailed information on how the library is constructed for the specific assay.

The following instructions use the 10X Genomics Chromium single cell gene expression 3' v3 chemistry as an example to illustrate how a prep kit tag library file is made in Partek Flow. Figure 1 is a schematic diagram of the single cell 3' v3.1 gene expression assay:

Click + Add prep kit button on Prep kit files tab at Library files management page, choose Other/Custom option from the Prep kit name drop-down list and specify a name e.g. Assay1 (Figure 2), choose the Build Prep kit option and click Create.

Select the Is paired end check button, and specify the information contained in each end:

Specify the new segment (Figure 4), choose Barcode from the Type drop-down list, specify the barcode .fasta file. If the barcodes are random with a fixed length, choose Arbitrary and specify the length. You can also choose the Manual option to manually add the barcode sequences that are available for this assay. Specify number of mismatches are allowed. Click Add

Click on the remove (-) icon to remove a segment if you make a mistake (Figure 5). Click on the + icon next to Barcode to add more segments, e.g. UMI.

According to the 10X 3' v3 assay, the UMI is a 12bp sequence (Figure 6).

Read 2 contains the 90bp insert sequence, click on the + icon next to Second mate segmentation, choose Insert from the Type drop-down list and specify the minimum read length allowed (Figure 7).

Check the Remove poly-A tail button and click Finish. The new prep kit file is added to the library file database in Partek Flow (Figure 8).

Click the three dots under Action, select View prep kit details to view the diagram (Figure 9).

When you perform the trim tag task on fastq files, Partek Flow will remove read 1 and the downstream alignment task will only be performed on read 2. The barcode and UMI information will be added in the read name in the output file for downstream analysis.

Additional Assistance

Create, view, and edit lists within a Partek Flow instance. To access Lists:

• Click the user avatar in the top right corner of the Partek Flow interface

• Choose Settings in the menu

• Select Lists from the left panel of the Components section.

Lists can be accessed by administrative and non-administrative users (Figure 1).

View and sort the name of the list, number of features, owner, and creation date by clicking the column title of the list table. Each list has the option to ignore and actions to download list, edit the list name or description, share list or delete the list.

Create a new list

To create new list, select the + New list button on the top of the page and give the list a name. Choose between the three list options:

• Local file: text file (.txt) on the local computer

• Text: manually specify a list of names

• Hosted lists: lists hosted on Partek website

When manually specifying a local file or text, only the user who added the list can view and use the lists. Hosted lists can be viewed and used by all of the users.

The list name needs to be unique for each user. A description is optional. The list of features can be specified from a .txt file on your local computer by selecting the Local file option (Figure 2). The .txt file should contain only one feature per row.

To manually enter a list of genes, select the Text option (Figure 3). Content can be typed into the text field or pasted from the clipboard as one feature per row.

Select Add list to add the list. The new list will be added to the list table.

When the Hosted lists option is chosen, lists can be downloaded from Partek (Figure 4).

Click the check box for each list on the left to select lists and click Add list. The downloaded lists are automatically shared with all users on the server. If you do not want to see the list when performing tasks related to lists (e.g. filter feature task), check the Ignore button.

Once a list is added to the Partek Flow server, it can be used to filter data (e.g. to filter quantified RNA-Seq data to only include or exclude the genes in a list) or to color by a feature list.

Use a Feature list to Select & Filter populations

Feature lists can be used to Select & Filter.

• In the Data Viewer, select the Style configuration option

• Choose Feature list from Color by drop-down list

• Select the List of interest using the drop-down

• Choose a Metric for the feature list

• Click Select & Filter under Tools on left

• Use the Add criteria drop-down to choose Gene score

• Use the slider or text fields to select a population

• Apply observation filter can then be used to filter this population to a specific node in the analysis pipeline

To remove this filter, click Clear filters.

Additional Assistance

The Pipelines management page allows users to view and manage the pipelines within a Partek Flow instance. To access the page, click the avatar on the top right corner, choose Settings, then select Pipelines on the left. This page can be accessed by administrative and non-administrative users. The table (Figure 1) shows a list of pipelines with their description, creation date, and the display name of the owner (the user who created or imported the pipeline). Non-administrative users can see pipelines created by other Partek Flow users in the table if the pipeline has been shared by the user. Administrative users can see all details.

Hiding Pipelines

All pipelines that have been created or imported within the same Partek Flow instance can be shared by all users. The pipeline manager allows each user to choose the pipelines that appear on their Task Menu. To hide a pipeline, select the corresponding checkbox in the Ignore column (Figure 1).

Downloading a pipeline

To download a pipeline, click the Download pipeline in the Actions column. A file with the extension *.pipeline will be download to the default download directory of your local computer.

Deleting a pipeline

Pipelines can be deleted by the owner (as listed in the Creator column) or by a user with admin privileges. Clicking Delete pipeline in the Actions column will delete the pipeline and it will no longer be available to any Partek Flow user. Note that deleting a pipeline affects all users of the same Partek Flow instance.

Importing a Pipeline

Within the Pipeline management page, you can upload a pipeline from your local computer or import a pre-built pipeline directly from the Partek website. You can import a pipeline even before you create or open a project within Partek Flow.

From My Computer

1. To import a .pipeline file from your local machine, click on the + Import pipeline button on the Pipelines management page

2. By default, the My computer option at the top of the Import pipeline page should already be selected. Click the + Choose button (Figure 2)

3. Browse to the location of the .pipeline file on your local machine and select it for upload. The selected file name will be displayed next to the Choose pipeline button

4. If you wish to give the pipeline a new name, type a new name into the Rename pipeline box and click Import

From Partek Website

1. To download a pipeline from the Partek website, click on the + Import pipeline button

2. Select Hosted pipelines (Figure 3). This will display all available pre-built pipelines from the Partek website.

3. Click the Import pipeline button next to the pipeline you wish to import (Figure 3). Alternatively, click Import all pipelines at the bottom of the page to import all pipelines displayed.

Additional Assistance

This document will show you how to delete an assembly and how to dissociate a library file.

Deleting an Assembly

To delete an assembly from the Library File Management, select the Delete assembly () icon by the assembly name. You will be prompted to confirm the deletion (Figure 1). If you also want to delete the individual library files from the disk, select the Delete the library files check box. Select Delete to proceed with deletion. Note that the deletion can not be un-done.

Disassociate Library Files

Individual library files can be removed by disassociating them from their respective assembly. To disassociate a file, click on Disassociate library file in the Actions column (Figure 2).

If the library file is used by multiple projects, the resulting dialog will provide a list of projects (Figure 3). As long as the library file is used, the Delete the library files option will be disabled.

Using the Dissociate library file tool does not physically remove the file from the disk, but disassociates the file from the selected library file name. This, in turn, enables you to associate newer or improved version of the library file with the same library file name. If the goal is to physically delete the library files from the disk, then all the projects using that library file must be deleted first.

Administrators of a Partek Flow server can manage access to files, folders and specific projects across all users of the server. These tools are particularly important in large organizations utilizing a shared server. This section details the following tools:

• User Management

• Group Management

• Licensing

• Directory Permissions

• Access Control Log

• Failed Logins

• Orphaned files

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow supports multiple user accounts, allowing you to keep your Partek Flow server secure and organized. This also facilitates data sharing and collaboration on projects. Administrative users have access to all parts of the software including server configuration, whereas non-administrative users only have access to the features necessary for data analysis. The first Partek Flow user account is created during installation, which is always an administrative user account.

Please note that Partek Flow users do not correspond to Linux or Mac users. A Partek Flow administrative account is not the same as a Linux ‘root’ user (see Glossary). All user accounts created in Partek Flow are internal to the Partek Flow server .

• User management page

• Creating a new Partek Flow user account using an LDAP database

• Creating a new Partek Flow user account without using an LDAP database

• Editing a Partek Flow user account

• Disabling a Partek Flow user account

• Transfer projects' ownership

User management page

To access the User Management page, click the avatar in the top right corner, choose Settings and click Users in the Access section on the left (Figure 1). This page can be accessed by administrative Partek Flow users only.

The number of available Partek Flow user licenses is displayed at the top of the User management page. This shows the number of user accounts that can be enabled. Administrative user accounts will not consume licenses, unless they become a member of any project, in which case they will consume a Partek Flow user licence. Please contact your account manager or email licensing@partek.com if you wish to increase the number of user licenses on your Partek Flow instance. If all available user licenses have been consumed, you will have to disable a user account before adding a new user. Disabled user accounts are easily re-enabled.

The table on the User management page displays user account information and status, with one user account per row. By default, the table will display all enabled users accounts that are online and offline. To change which users are displayed, select or deselect the checkboxes above the table (Figure 1).

By clicking on the Send message button at Actions column, the administrative user can send an e-mail notification about account creation (Figure 2). The email template depends on the user database, i.e., within an LDAP or not within an LDAP database (vide infra).

If multiple Partek Flow users are logged into an instance at the same time, administrative users have the ability to log them out by clicking the Log out user button at Actions column. If a user is logged out by an administrator and the user has tasks running or in the queue, those tasks will continue to run.

Creating a new Partek Flow user account using an LDAP database

New Partek Flow user accounts can be created using username and password credentials from a Lightweight Directory Access Protocol (LDAP) database, if configured. You can create user accounts without using an LDAP database too.

1. Click the + Add new user at the top of the User management page

2. Select a Source for LDAP database from the drop down list in the Add user dialog (Figure 3)

3. Start typing a few characters of the username you wish to add in the Username box and Partek Flow will suggest users that are available on your LDAP database. Select one of the suggested usernames and the Username, Display name and Email will autocomplete. You can change the Display name if necessary

4. There may be more than one email address associated with a user in the LDAP database, so choose the correct one from the Email drop-down list

5. To give the new user account administrative privileges, select the Administrator checkbox (optional)

6. The new user account can also have a Private directory. If so, then that directory will be the default output directory for the users and all the project directories will be created underneath it. The user will be the only one with the access to the directory specified in the dialog box, unless permissions (to either the Private directory or one if its parents) are given using Directory permisions.

7. To set a disk space usage limit on the new user account, select the Disk quota radio button and type in the disk quota limit in GB (optional). This limit includes input and output files across all projects the new user will own. To allow unrestricted disk usage, select the None radio button. Disk quota preferences can be managed on the System preferences page. Note that setting disk quotas require an enterprise license

8. Click Save

The new user account will be active immediately. The new user can log into the Partek Flow instance using the same username and password as their email account. Please note, the new user will not be able to manage their username and password settings from within Partek Flow, as this is determined by the LDAP server.

Creating a new Partek Flow user account without using an LDAP database

1. Click the + Add new user at the top of the User management page

2. Select Source in the Add user dialog

3. Type a username, display name and email address in the respective fields

4. To give the new user account administrative privileges, select the Administrator checkbox (optional)

5. To set a disk space usage limit on the new user account, select the Disk quota radio button and type in the disk quota limit in GB (optional). This limit includes input and output files across all projects the new user owns. To allow unrestricted disk usage, select the None radio button. Disk quota preferences can be managed on the System preferences page. Note that setting disk quotas require an enterprise license

6. Click Save

The screen will return to the User management page and there will be a message at the top of the screen (Figure 4). The new user needs to click on the link sent via email and follow the on-screen instructions for creating a password.

Editing a Partek Flow user account

To edit user account details, click on the Edit account next to the user account in the Actions column (Figure 1). This will open the same dialog as in Figure 3, with the user account details filled out. An administrative user can make the necessary changes and click Save. Users can also edit some of their own details Personal settings.

Disabling a Partek Flow user account

To disable a user account, deselect the checkbox in the Status column in the table on the User management page (Figure 5). The user account will then disappear from the table. If a user account if disabled while the user is logged in, they will immediately be logged out.

If a user account is disabled and they have tasks running or in the queue, you will be asked if you want to cancel them (Figure 6).

If a user tries to log into the Partek Flow instance and their account has been disabled, they will see a warning message (Figure 7).

Users that have had their account disabled will no longer appear as a member of a project on the Home page. Under the Project settings tab of a project, their username and avatar will still be shown, but with a strikethrough (Figure 8).

To display disabled user accounts, select the Disabled from the Status drop down list in the table (Figure 9). Disabled accounts can be easily re-enabled by selecting the check box in the Status column.

Transfer projects' ownership

When a user is no longer a user on this Partek Flow instance, for instance, the user left the insititue, all the projects he created can be transfered to another user by clicking Transfer Projects' ownership (Figure 10).

Specify the old owner username and new owner name, click Transfer projects button.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow allows you to configure advanced settings for various tasks including adapter trimming (Cutadapt), alignment (various aligners), quantification (Cufflinks), differential gene expression analysis (GSA, ANOVA and Cuffdiff), variant detection (Partek, samtools and Freebayes) and variant annotation (SNPEff). User-defined option sets can be saved and applied to other projects.

This user guide will cover the following topics:

• Saving a Custom Option Set

• Option Set Management Page

• Adding an Option Set from the Command Line

Saving a Custom Option Set

A Bowtie alignment task will be used as an example, but the steps are the same for any task that allows configuration of advanced settings. Click Configure in the Advanced options section on the Task setup page (Figure 1).

Name the new custom option set, add a description (optional) and click Save in the New option set dialog (Figure 3).

The saved option set will appear in the drop-down list in the Advanced options section on the Task setup page (Figure 4). All saved option sets are available to all of the users of the same Partek Flow instance.

Option Set Management Page

To access the Option set management page, click the avatar in the top right corner, choose Settings and click Option sets under Components section on the left (Figure 5). This page can be accessed by administrative and non administrative Partek Flow users.

Choose a task from the selector and all associated option sets will be shown in a table (Figure 5). Click the three dots in the Actions column and select View parameters to display the option set (Figure 6). Select Delete option set in the Actions column to delete an option set. Note that only the Partek Flow user who created an option set and administrative Partek Flow users are able to delete an option set.

Adding an Option Set from the Command Line

This is a Partek Flow licensed feature separate from the base license.

User-defined command lines can be copied and pasted to create a custom option set. This is particularly useful if, for example, you have previously run an alignment with custom options on the command line and wish to use the same set of options for an alignment in Partek Flow.

On the Option set management page, click the + Add option set from command line button (Figure 5). In the Add option set dialog (Figure 7), choose a task from the Select Task drop-down list and the version number (if applicable). Name the option set by typing into the O_ption set name_ box. Add a description of the option set by typing into the Option set description box (optional). Paste the command line from the clipboard into the Command line box and click Save.

The command line will be parsed, validated and converted into a Partek Flow option set. The Command line parsing report will summarize the Command, Recognized parameters and Ignored parameters (Figure 8). Partek Flow will ignore parameters with a syntax error or parameters already dealt with by other components of the software (e.g. input/output file paths, performance optimization). Click OK to close the report. The option set will now appear on the Option set management page (Figure 5) and can be applied to projects (Figure 4).

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

To access the Licensing page, select the avatar in the top right corner, choose Settings and select Licensing on the left (Figure 1). This page can be accessed by administrative Partek Flow users only.

This page displays the status of all license features and toolkits, including their expiration dates. If a license needs to be updated, copy and paste the new license key into the License key box and select the Update button. For your convenience, the Partek product and Host ID information is displayed on the screen. If you need a new license key, this information can be copied and sent to .

For additional information about the licensing features and toolkits, please see . Alternatively, please contact your account manager.

Additional Assistance

Partek Flow can be configured to permit specific user access to directories listed in the Directory permissions page.

Directory browsing permissions

When the Enforce permissions checkbox (Figure 1) is selected, the only directories that users can access are those listed under the Directory column. Access means being able to see the directory when browsing, so that files can be created in it or selected from it. This permission is recursively applied to any subfolder of the listed directory.

The enforced permission can be applied to a specific user, several users, or a group (shown under the Users column). Access for each directory can be edited or revoked by selecting the edit or delete Action icons, respectively. Note that files already part of a project can always be analyzed by the collaborators of that project.

This feature is particularly important for creating isolated directories for each user. For more information on setting-up isolated directories, please refer to the documentation on .

To permit access to a new directory, click the Permit access to a new directory button. This will bring up the Add directory permissions window (Figure 2).

Browse to the desired directory or create a new folder. Using the arrow buttons, select the users that will be granted access to that folder. Alternatively, if you want all users to access the folder (such as folders for shared reference genome or gene annotation files), select the All users checkbox.

Directory reassignment

If a specific directory containing files used by Partek Flow (such as raw data files) has been renamed or moved, you can use the Directory reassignment tool to ensure Partek Flow can continually access relevant files. Enter the former and current directory paths to reassign them.

Additional Assistance

Access control log is administrative tool giving an overview of Partek Flow users' access privileges. The tool focuses on activities related to and Group management. To invoke it, first log in as a user with administrative privileges and then go to Settings > Access management > Access control log. Example report is given in Figure 1.

The first column (Time) contains the timestamp of the activity. Column Changer shows you the display name of the Partek Flow user who changed the access along with their permanent numeric identifier (parenthesized). The current display name of the changed user, as well as the matching numeric ID, can be seen in the Object column. Finally, the change made to the object, followed by the project (the number in the parenthesis is the change counter), role or privilege is listed in the Change column. Text boxes on top of each column are search tools, while the arrows icon enables to sort the column ascending or descending.

Additional Assistance

Partek Flow users can be organized into groups. For example, user accounts can be organized by research group, privilege level (e.g. administrative vs non-administrative) or by pre-defined groups determined by a database. This enables easier among multiple Partek Flow users and makes it easier to define for groups of users. For editions, administrative users can generate usage report per group and reserve a number of concurrent licenses for groups.

Group Management Page

To access the User Management page, click the avatar in the top right corner, choose Settings and click User management on the left (Figure 1). This page can be accessed by administrative and non-administrative Partek Flow users.

Creating a Group

Owner – choose the owner of the group from the drop-down list of Partek Flow users. Alternatively, start typing a few characters of the users’ display name and Partek Flow will suggest users that are available for you to choose.

Source is … – this checkbox is only available to administrative users. Select this check box if you want to create a group based on the configured LDAP database. Leaving this checkbox unselected means the group will be created and managed entirely within Partek Flow.

Group name – if the source is an LDAP database, start typing a few characters of the group name and Partek Flow will suggest available groups for you to choose. If the group is managed entirely within Partek Flow, simply type the name of the new group.

Display name – only visible if the source is an LDAP database. If you want the LDAP group name to appear differently in Partek Flow, type in an alternative name. If you want the LDAP group name to appear the same in Partek Flow, leave this field blank.

Additional Assistance

Orphaned files are files that were previously imported into projects or generated by project tasks but were left behind when the projects or tasks were deleted. They no longer belong to any projects but still consume disk space, which counts against any server quota, though not individual user quotas. If you transfer files to Flow server outside Partek Flow, for instance when you use SFTP access to the server, before the files got imported into any projects, those transferred files are also considered as orphaned files. If you use Transfer files function within Flow, the files are not considered orphaned files.

In the orphaned file table, each row is a file, file name including the path, creator and size of the file will be displayed. Click on the Delete file in the Actions column to delete a file on that row in the table (Figure 1). If you search for a file name/folder name or creator by typing in the search box on the upper-right corner above the table, the table will display only the files containing the searched keyword.

The Delete all filtered orphaned files button (Figure 1) will delete all the files displayed in the current table. If you want to clean up all the files within a certain project output folder, search for the folder name and click "Delete all filtered orphaned files". However it is always a good idea to check all the files before delete.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

The System queue page gives you the list of system-related tasks performed on your Partek Flow server (Figure 1). These tasks generally benefit all the users of the server. They include, but are not restricted to, downloading annotation databases and building aligner indexes.

Filter to a specific task by entering keywords in the Task search box. Use the drop-down menu under the corresponding column header to filter tasks to specific users/date ranges and statuses. The progress of ongoing system tasks is displayed as a bar in the Status column. Cancel any ongoing task by clicking the button.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Click the + Add reference files button under the Reference Files section header and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 1). If a cytoband file is already associated with an assembly, Reference sequence will be the only option available in the Add reference sequence dialog and will not appear in a drop-down list (Figure 1).

If you are using an assembly supported by Partek (e.g. human), select Download reference sequence and click Create to get the reference sequence from the Partek repository. Alternatively, select Import reference sequence and click Create to add the reference sequence from another source.

If you are using a custom assembly (e.g. for a non-model organism), the Download reference sequence option will not be available (Figure 2).

The Import reference sequence option allows you to add a reference sequence from the Partek Flow Server or a URL download link (Figure 3).

To add a reference sequence from the Partek Flow server, select Partek Flow Server, click Browse icon and navigate to the directory storing the reference sequence file(s) (Figure 4). Only files with the correct file extensions (.fa, .2bit or any compressed format) will be displayed in the file browser. Select the checkbox next to the file name(s) you wish to import and click Continue (Figure 4). Click Finish to add the selected reference sequence file(s).

To upload a reference sequence from your local computer, click Transfer files to the server, click Transfer files, drop files to the Transfer files dialog or click My Device and navigate to the location of the file(s) on your local machine (Figure 5). Click Upload to complete the file upload. Do not exit the browser tab or let the computer go to sleep or shut down until the transfer has completed.

To download a reference sequence (e.g. from a public repository such as ENSEMBL), select URL and input the URL address (Figure 6). Make sure to include the full URL address, starting with the transfer protocol (e.g. http:// or ftp://) and ending with the file name. It is advisable to find the download link address, copy it to the clipboard and paste it into the Input URL box. Click Finish to add the selected reference sequence file(s) (Figure 6).

Note that you can specify multiple fasta files (e.g. one file per chromosome) and Partek Flow will concatenate them. If a fasta file is imported, a 2bit version of the file will automatically be created and vice-versa. Partek Flow will also accept a range of compressed file formats (gzip, bzip2, zip, tar). If a compressed file is imported, it will automatically be uncompressed and processed.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow gives you the ability to evaluate and modify the hardware resources available for analysis, track system tasks, and, with the purchase of a Usage report license, generate usage reports for your Partek Flow instance. These options are located in the Settings menu. This document will describe the following sections:

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

The System resources page gives users information about the hardware resources available for use in their Partek Flow server.

The Queue status section indicates the number tasks currently running as well as the number of waiting tasks. These include tasks that are waiting for system resources to be available or for an upstream task to complete. Queue will empty by gives an estimated time of completion for all queued tasks. Click on the button to display queued tasks.

The Licensing section summarizes the number of Available cores licenses and Available worker licenses. Contact your Account Manager to obtain additional core or worker licenses.

The Active workers table lists one active worker node per row (an example with a single worker is shown in Figure 1) and contains performance metrics for worker processes and server processes. The columns provide the following information:

• Name: worker’s identifier (IP address or name)

• CPU usage: the computational load of the worker process

• Memory usage: the memory usage of the worker process

• Machine capacity: indicates the number of cores and amount of RAM available to the worker

• Uptime: the duration that the worker has been running

• Type: the type of worker (described below)

Partek Flow supports two types of workers: Partek Flow is installed on the server while those labeled worker run on a remote machine. When the server is configured to accept work, its type is changed to internal to differentiate it from other workers. Multiple workers can be deployed to handle computationally-intensive tasks or to help alleviate a long queue of tasks. Figure 3 shows an example with five active workers.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow supports multiple versions of analysis tools, including third-party software (e.g. aligners). By default, the most recent versions are implemented during installation of Partek Flow. In some circumstances, you may need to use a different version of a tool, e.g. if reproducing an older study. Furthermore, tasks can be enabled and disabled.

Task Management Page

Only Partek Flow users with administrator privileges have access to the Tasks management page. Changes made on this page are applied to all other users on the Partek Flow instance. To access the page, click the avatar in the top right corner, choose Settings and click Tasks on the left (Figure 1).

To enable or disable a task, select or deselect the checkbox next to the Task name on the Tasks management page, respectively (Figure 1).

To change the version of a task, click the drop-down and choose a different version from the drop-down list (Figure 2). All tasks launched after the change will use the chosen version.

To review which version has been used to perform a task, hover the cursor over the task node and inspect the pop-out balloon (Figure 3). Alternatively, the version number is shown on the Task details (Figure 4) page and the Data summary report (Figure 5).

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The Usage report section requires a Usage report license and is only available for user accounts with Administrator status. This section allows you to create customized reports on certain usage statistics such as disk usage and project count. These reports can be drafted for a certain date range, allowing you to monitor resource usage over defined periods of time.

The Saved reports section lists previously-generated usage reports that have been saved by the user (Figure 1). These can be used to review former reports generated. Click on the button to delete any saved reports.

To generate a usage report, go to the Generate report section. Select the following:

• The metric you would like reported (Report)

• How you would like the information grouped (For each)

• The Date range to be reported

For instance, Figure 2 shows the creation of a disk usage report for each project within a custom date range.

After selecting your options, click the Generate report button. The usage report will be displayed at the bottom of the page as a table (Figure 3). Click on the Save report link at the lower left corner of the table to save the report. To download the report as a tab-delimited text file, click the Download link at the lower right corner of the table.

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Failed logins is an administrative tool providing an overview of login attempts that were not successful. To invoke it, first log in as a user with administrative privileges and then go to Settings > Access management > Failed logins. Example report is given in Figure 1.

Each row of the table is a single failed login attempt; the time is given in the first column, the display name that was typed in on the login screen in the second column, and the reason for the failure in the third column. Possible reasons are: Invalid credentials, No concurrent license available, and Limited to administration.

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