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The Partek Flow Metadata Tab has an option to import data, and is where sample/cell attributes are managed. This is also where users can modify the location of the project output folder.
The Metadata tab can be used to import data. To add samples to the project, click Add data under Import, different import options are displayed using the cascading menu (Figure 1).
This method adds samples by creating them simultaneously as the data gets imported into a project. The sample names are assigned automatically based on filenames.
Before proceeding, it is ideal that you have already transfer the data you wish to analyze in a folder (with appropriate permissions) within the Partek Flow server. Please seek assistance from your system administrator in uploading your data directly.
Select the Automatically create samples from files button. The next screen will feature a file browser that will show any folders you have access to in the Partek Flow server (Figure 2). Select a folder by clicking the folder name. Files in the selected folder that have file formats that can be imported by Partek Flow will be displayed and tick-marked on the right panel. You can exclude some files from the folder by unselecting the check mark on the left side of the filename. When you have made your selections, click the Create sample button.
Alternatively, files can also be uploaded and imported into the project from the user's local computer -only use this option if your file size is less than 500MB. Select the My computer radio button (Figure 3) and the options of selecting the local file and the upload (destination) directory will appear. Only one file at a time can be imported to a project using this method.
Multiple data files can be compressed a single .zip file before uploading. Partek Flow will automatically unzip the files and put them in the upload directory.
Please be aware that the use of the method illustrated in Figure 3 highly depends on the speed and latency of the Internet connection between the user's computer and the server where Partek Flow is installed. Given the large size of most genomics data sets, is not recommended in most cases.
After successful creation of samples from files, the Data tab now contains a Sample management table (Figure 4). The Sample name column in the table is automatically generated based on the filenames and the table is sorted in alphabetical order.
Clicking the on the** Show data files** link on the lower right side of the sample management table will expand the table and reveal the filenames of the files associated with each sample. Conversely, clicking on Hide data files will hide the file information.
The columns in the expanded view show the files associated with each sample. Files are organized by file type. Any filename extensions that indicate compression (such as .gz) are not shown.
Once a sample is created in a project, the files associated with it can be modified. In the expanded view, mouse over the +/- column of a sample. The highlighted icons will correspond to the options for the sample on that row.
Samples can be added one at a time by selecting the Create a new blank sample option (Figure 5). In the following dialog box, type a sample name and click Create. This process creates a sample entry in the sample management table but there is no associated file with it, hence it is a "blank sample."
Expanding the Sample management table by clicking Show data files on the lower left corner of the table will reveal the option to associate files to the blank sample.
Alternatively, if you have a matrix of data, such as raw read count data in text format, select Import count matrix. The requirements of this text file are listed below:
The file contains numeric values in a tab-delimited format, samples can be on rows while features (e.g.gene names) are in columns, or vice versa
The file contains unique sample IDs and feature IDs
If the data contains sample attribute information, all these attributes have to be ether
The leftmost columns when samples are on rows (Figure 6)
The first few rows when samples are on columns (Figure 7)
Like all other input files, you can upload the file from the Partek Flow server, My Computer or via a URL. Uploading the file brings up a file preview window (Figure 8). The preview of the first few rows and columns of the text file should help you determine on which rows/columns the relevant counts are located (the preview will display up to 100 rows and 100 columns). Inspect the text preview and indicate the orientation of the text file under File format>Input format.
If the read counts are based on a compatible annotation file in Partek Flow, you can specify that annotation file under Gene/feature annotation. Select the appropriate genome build and annotation model for your count data. Select the Contain sample attributes checkbox if your data includes additional sample information.
The example above is showing an example text file with samples listed on rows. The gene ID is compatible with the hg19 RefSeq Transcripts - 2016-08-01 annotation model. Under the Column information and Row information sections, indicate the location of the Sample ID, which in this case is on Column 1. Indicate the sample attribute location by marking where it starts, which in the example is at Column 2. Mark the Feature ID, which in this case are gene IDs and starts at Column 4.
If the data has been log transformed, specify the base under Counts format.
The project output directory is the folder within the Partek Flow server where all output files produced during analysis will be stored.
The default directory is configured by the Partek Flow Administrator under the Settings menu (under System Preferences > Default project output directory).
If the user does not override the default, the task output will go to a subdirectory with the name of the Project.
After samples have been added in the project, additional information about the samples can be added. Information such as disease type, age, treatment, or sex can be annotated to the data by assigning the Attributes for each sample.
Certain tasks in Partek Flow, such as Gene-Specific Analysis, require that samples be assigned attributes in order to do statistical comparisons between groups or samples. As attributes are added to the project, additional columns in the sample management table will be created.
Attributes can be managed or created within a project. Under the Data tab, click the button to open the Manage attributes page (Figure 9).
To prepare for later data analysis using statistical tools, attributes can either be categorical or numeric (i.e., continuous).
For categorical attributes, there are two levels of visibility. Project-specific categorical attributes are visible only within the current project. System-wide categorical attributes are visible across all the projects within the Partek Flow server, and are useful for maintaining uniformity of terms. Importing samples in a new project will retain the system-wide attributes, but not the project-specific attributes.
A feature of Partek Flow is the use of controlled vocabulary for categorical attributes, allowing samples to be assigned only within pre-defined categories. It was designed to effectively manage content and data and allow teams to share common definitions. The use of standard terms minimizes confusion.
To add a categorical attribute in the Manage attributes page, click the Add new attribute (Figure 10). In the dialog box, type a Name for the attribute, select the Categorical radio button next to Attribute type, select the visibility of the attribute and then click the Add button.
Repeat the process for additional attributes of the samples in your study. When done, click Back to sample management table. Categorical attributes will default to Project-specific visibility.
Click an attribute name to drag and drop can change the order of the attributes displayed on the data tab. Click on group name to drag and drop vertically can change the order of the group name, which can be reflected on visualization.
To add a numeric attribute in the Manage attributes page, click the Add new attribute. In the dialog box (Figure 13), type a Name for the attribute, select the Numeric radio button next to Attribute type, and then click the Add button. Some optional parameters for numeric attributes include the Minimum value, Maximum value, and Units. When done, click Add to return to the Manage attributes page. Repeat the process add more numeric attributes. When done, click Back to sample management table.
Since system-wide attributes do not have to be created by the current user, they only need to be added to the sample management table in a project.
In the Data tab, click Add a system-wide attribute button. In the dialog box that follows (Figure 14), a drop down menu is located next to Add attribute where you can select the System-wide attribute you would like to add to the project. Once selected, it will be recognized automatically as either Categorical, system-wide or the Numeric attribute.
For an System-wide categorical attribute, the different categories are listed and you have the option of pre-filling the columns with N/A (or any other category within the attribute). Click Add column and you will return to the Data Tab.
After adding all the desired attributes to a project, the sample management table will show a new column for each attribute (Figure 15). The columns will initially as "N/A", as the samples have not yet been categorized or assigned a value. To edit the table, click Edit attributes. Assign the sample attributes by using a drop down for categorical attributes (controlled vocabulary) or typing with a keyboard for numeric attributes.
When all the attributes have been entered, click Apply changes and the sample management table will be updated. After editing the sample table, make sure there are no fields with blank or N/A values before proceeding. To rename or delete attributes, click Manage attributes from the Data tab to access the Manage attributes page.
Another way to assign attributes to samples in the Data tab is to use a text file that contains the table of attributes and categories/values. This table is prepared outside of Partek Flow using any text editing software capable of saving tab-separated text files.
Using a text editor, prepare a table containing the attributes. An example is shown in Figure 16. There should only be one tab between columns with no extra tabs after the last column. In this particular example, the first column contains the filename and the text file is saved as Sampleinfo.txt.
The first row of the table in the text file contains the attributes (as headers). The first column of the table in the text file, regardless of the header of the first column, should contain either the sample names or the file names of the samples already added in Partek Flow. The first column is the unique identifier that will match the samples to the correct values or categories.
To upload sample attributes, click Assign sample attributes from a file in the Data tab. Then indicate where the attribute text file is stored and navigate to it. Partek Flow will parse the text file and present attributes that will be available for import (Figure 17).
Select the attributes you want to import by clicking the Import check box. Imported attributes that do not currently exist in the project will create new project-specific attributes.
You can change the name of a specific attribute by editing the Attribute name text box. Columns containing letter characters are automatically selected as categorical attributes. Columns containing numbers are suggested to be numeric attributes and can be changed to categorical using the drop down menu under Attribute type.
The first column is always the unique identifier and can refer only to File names or Sample names.
If using Sample names in the first column, they must match the entries of the Sample name column in the Sample management table.
If using File names in the first column, use the filenames shown in the fastq column of the expanded sample management table (see Figure 4) then add the extension .gz. All filenames must include the complete file extension (e.g., Samplename.fastq.gz).
The header name of the first column of the table (top left cell of our text table) is irrelevant but should not be left blank. Whether the first column contains File names or Sample names will be chosen during the process.
The last column cannot have empty values
Missing data (blank cells) can only be handled if the attribute is numeric. If it is categorical, please put a character in it.
It is advisable to use Sample name as the first column identifier when:
Samples are associated with more than one file (for instance, paired-end reads and/or technical replicates).
The files were imported in the SRA format (from the Sequence Read Archive database). In Partek Flow, they are automatically converted to the FASTQ format. Consequently, their filenames would change once they are imported. The new file names can be seen by expanding the sample management table, the new extension would be .fastq.gz.
If attributes are assigned from two different text files, the following will happen:
If the previous attributes have the same header and type (both are either categorical or numeric), the values are overwritten.
If there are different/additional headers on the "second round" of assignment, these new attributes will be appended to the table.
For numeric attributes, a "blank" value will not override a previous value.
The attributes assigned to the samples within the Data Tab will be associated with the samples throughout the project. During the course of analysis, Partek Flow tasks generate various tables and any attributes associated with a sample can be included in the table as optional columns. An example is shown in Figure 18 for a pre-alignment QA/QC report where the Optional columns link on the top left of the table reveal the different sample attributes.
In the Data tab, each sample can be renamed or deleted from the project by clicking the gear icon next to the sample name. The gear icon is readily visible upon mouse over (Figure 19). Sample can only be deleted if no analysis has been performed on the data yet. If any analysis has been performed on the data node, then delete sample operation is invisible. You can perform filter samples in downstream analysis if you want to exclude certain samples in further analysis. Deleting a sample from a project does not delete the associated files, which will remain on the disk.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Partek Flow software manages separate experiments as projects. A complete project consists of input data, tasks used to analyze the data, the resulting output files, and a list of users involved in the analysis.
This chapter provides instructions in creating and analyzing a project and covers:
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Using a web browser, log in to Partek Flow. From the Home page click the New Project button; enter a project name (Figure 1) and then click Create project.
The Project name is the basis of the default name of the output directory for this project. Project names are unique, thus a new project cannot have the same name as an existing project within the same Partek Flow server.
Once a new project has been created, the user is automatically directed to the Analysis tab of the Project View (Figure 2).
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
The Log tab contains a table of the tasks that are running, scheduled, or those that have been completed within the Partek Flow (Figure 1). It provides an overview of the task progress, enables task management, and links to detailed reports for each task.
Each row of the table corresponds to a task node in the Analyses tab. The list can be sorted according to a specific column using the sort icon .
The Task column lists the name of the tasks. On the left of the task name is a colored circle indicating the layer of this task. The column is searchable by task name. Clicking the task name will open the Task report page. If the task did not generate a report, the link will go to the Task details page.
The User column identifies the task owner. Aside from the user who created the project, only collaborators and users with admin privileges can start tasks in a project. Clicking a name in the User column will display the corresponding User profile.
The End column shows when the task was completed. It will show the actual time for completed tasks, and the estimated time for running tasks. These estimates improve in accuracy as more tasks are completed in the current Partek Flow instance.
The Status column displays the current status of the task, such as Waiting, Running, Done, Canceled. If the task is currently running, a status progress bar will appear in the column. Once completed, the status of a task will be Done and the End column will be updated with the completion time.
The Project details section shows the Name of the project as well as (optional) a textual project Description and a Thumbnail (picture) (Figure 1).
The owner and collaborators (if any) can customize the Description and Thumbnail entries by pushing the orange Edit project details button (Figure 2). The fields can now be edited to:
Rename the project (names are limited to 30 characters). The original project Name is the one selected when creating the project
Add or change a project description (up to 2000 characters)
Add or change a thumbnail of the project (supported formats are .jpg, .bmp, .gif, .png; the maximum size of the image file is 10 MB)
The Description accepts hyperlinks starting with "http://" or "https://" and if selected, will open a new tab browser to navigate to the website. This description will be also displayed to collaborators and administrators on the Partek® Flow® Home Page. Choose File button launches a file browser showing directory structure of the local computer from which the thumbnail image file will be uploaded. Alternatively, Clear thumbnail button removes the current thumbnail.
Once all the edits have been made, push Save to accept (or Cancel to reject).
If a thumbnail has been added, it will appear on the Project details tab (Figure 3) and on the home page of Partek Flow, on the Details tab of the project.
The Members section provides an overview of users associated with a particular project and enables project creators (owners) and administrators to add collaborators (Figure 1). A user (without administrator status) has to be specified as a collaborator in a project to be able to access the project in his/her home folder and to perform tasks.
Pushing the pencil icon (Pencil icon](../../../.gitbook/assets/pencil-icon.png)) by a project member can result in two dialogs, depending on the status of the member. For a collaborator or a viewer, the pencil icon changes the member's role (e.g. from a Viewer to a Collaborator) (Figure 4).
Moreover, the project owner can transfer the ownership to another user account (one of the accounts already available at the current instance of Partek Flow) using the New owner dropdown list (Figure 5). The previous (old) owner can remain as a project collaborator, with the help of the matching option.
If email notifications are turned on for project ownership transfer, an email dialog box appears. This can be used to add additional text to the notification email body (Figure 6).
After samples have been added and associated with valid data files, in a Partek Flow project, a data node will appear in the Analyses tab (Figure 1). The Analyses tab is where different analysis tools and the corresponding reports are accessed.
The Analyses tab contains two elements: data nodes (circles) and task nodes (rounded rectangles) connected by lines and arrows. Collectively, they represent a data analysis pipeline.
Data nodes (Figure 2) may represent a file imported into the project, or a file generated by Partek Flow as an output of a task (e.g., alignment of FASTQ files generates BAM files).
Missing image Figure 2. The Analyses tab showing a data node of unaligned reads
Task nodes (Figure 3) represent the analysis steps performed on the data within a project. For details on the tasks available in Partek Flow, see the specific chapters of this user manual dedicated to the different tasks.
Clicking on a node reveals the context sensitive menu, on the right side of the screen.
Only the tasks that are available for the selected data node will be listed in the menu. For data nodes, actions that can be performed on that specific data type will appear.
In Figure 4, a node that contains Unaligned reads is selected (bold black line). The tasks listed are the ones that can be performed on unaligned data (QA/QC, Pre-analysis tools, and Aligners).
After a task is performed on a data node, a new task node is created and connected to the original data node. Depending on the task, a new data node may automatically be generated that contains the resulting data. For details of individual tasks, see Task Menu.
In Figure 5, alignment was performed on the unaligned reads. Two additional nodes were added: a task node for Align reads and an output data node containing the Aligned reads.
To run a task, select a data node and then locate the task you wish to perform from the context sensitive menu. Mouse over to see a description of the action to be performed. Click the specific task, set the additional parameters (Figure 6), and click Finish. The task will be scheduled, the display will refresh, and the screen will return to the project's Analyses tab.
In Figure 6, the STAR aligner was selected and the choices for the aligner index and additional alignment options appeared.
Tasks that are currently running (or scheduled in the queue) appear as translucent nodes. The progress of the task is indicated by the progress bar within the task node. Hovering the mouse pointer over the node will highlight the related nodes (with a thin black outline) and display the status of the task (Figure 7).
If a task is expected to generate data nodes, expected nodes appear even before the task is completed. They will have a lighter shade of color to indicate that they have not yet been generated as the task is still being performed. Once all tasks are done, all nodes would appear in the same shade.
Tasks can only be cancelled by the user that started the task or by the owner of the project. Running or pending tasks can be canceled by clicking the right mouse button on the task node and then selecting Cancel (Figure 8). Alternatively, the task node may be selected and the Cancel task selected from the context sensitive menu.
A verification dialog will appear (Figure 9) asking to confirm the task cancellation, the cancelled tasks will remain in the Analyses tab but will be flagged by gray x circles on the nodes (Figure 10).
Data nodes connected to incomplete tasks are also incomplete as no output can be generated (Figure 10).
To delete tasks from the project click the right mouse button on the task node and then select Delete (Figure 11). Alternatively, click the task node and select Delete task from the context sensitive menu.
Selecting a task node will reveal a menu pane with two sections: Task results and Task actions (Figure 13).
Items from the Task results section inform on the action performed in that node. Certain tasks generate a Task report (Figure 14), which include any tables or charts that the task may have produced.
The Task details shows detailed diagnostic information about the task (Figure 15). It includes the duration and parameters of the task, lists of input and output files, and the actual commands (in the command line) that were run.
Additionally, the Task details page would contain the error logs of unsuccessful runs. The user can download the logs or send them directly to Partek. This page plays an important role in diagnosing and troubleshooting issues related to task.
Double clicking on a task node will show the Task report page. However, if no report was generated, the user will be directed to the Task details page.
In the Task actions sections, the selected task can be Re-run w/new parameters, and in case it is part of a pipeline that includes additional tasks after it, running the Downstream tasks is an option. Re-running tasks will result in a new layer being made in the Analyses tab.
Another action available for a task node is Add task description (Figure 16), which is a way to add notes to the project. The user can enter a description, which will be displayed when the mouse pointer is hovered over the task node.
It is common for next-generation sequencing data analysis to examine different task parameters for optimization. Users may want to modify an upstream step (e.g. alignment parameters) and inspect its effect on downstream results (e.g. percent aligned reads).
The implementation of Layers makes optimizations easy and organized. Instead of creating separate nodes in a pipeline, another set of nodes with a different color is stacked on top of previous analyses (Figure 17). To see the parameters that were changed between runs, hover the mouse icon over the set of stacked task nodes and a pop-up balloon will display them. The text color signifies the layer corresponding to a specific parameter.
Layers are formed when the same task is performed on the same data node more than once. They are also formed when a task node is selected and the Re-run it w/new parameters is selected in the context sensitive menu. This will allow the users to change the options only for the selected task. The user may choose to re-run the task to which the changes have been made, as well as all the downstream tasks until the analysis is completed. To do so, select Re-run w/new parameters, downstream tasks from the context sensitive menu.
To select a different layer, use the left mouse button to click on any node of the desired layer. All the nodes associated with the selected layer have the same color and when clicked will be displayed on the top of the stack.
Addition of task and resulting data nodes to project may lead to creation of long pipelines, extending well beyond the border of the canvas (Figure 18).
In that case, the pipeline can be collapsed, to hide the steps that are (no longer) relevant. For example, once the single-cell RNA-seq data has been quantified, Single cell counts data node will be a new analysis start point, as the subsequent analyses will not focus on alignment, UMI deduplication etc. To start, right-click on the task node which should become a boundary of the collapsed portion of your pipeline and select Collapse tasks (Figure 19).
All the tasks on that layer will turn purple. Then left-click the task which should be the other boundary of the collapsed portion. All the tasks that will be collapsed will turn green and a dialog will appear (Figure 19). In the example shown in Figure 19, the tasks between Trim tags and Quantify barcodes will be collapsed. Give the collapsed section a name (up to 30 characters) and select Save (Figure 20).
The collapsed portion of the pipeline is replaced by single task node, with a custom label ("Single cell preprocessing"; Figure 21).
To re-expand the pipeline double click on the task node representing the collapsed portion of the pipeline. Alternatively, single click on the node and select Expand... on the context-sensitive menu. Within the same menu, you can also preview the contents of the collapsed task by selecting View... (Figure 22).
The Attachments tab allows the project owner to add external (i.e. non-Partek Flow) files to a project (for instance, spreadsheets, word documents, manuscripts). To attach a file, go to the Attachments tab (Figure 1). Choose File button invokes the file browser showing the directory structure of the local computer. Select the file that you want to attach and then click on the Upload attachment button. For security reasons, Partek Flow will not allow you to add an executable file.
All added files will be listed in the table under the Attachments tab (Figure 2). The tab will also display file sizes, the user name of the person who uploaded the file and the time it was uploaded. Note that uploaded files will count towards the total size of the project, and thus, if available, to the disk quota of the project owner.
To remove a file, click the icon. To download the attachment, click the icon.
Click the green icon ( ) to associate additional files or the red icon ( ) to dissociate a file from a sample. You can manually associate multiple files with one sample. Dissociating a file from a sample does not delete the file from the Partek Flow server.
Mouse over the +/- column and click the green icon ( ) to associate a file(s) to the sample. Perform the process for every sample in your project.
The user has the option of specifying an existing folder or creating a new one as the project output directory. To do so, click the icon next to the directory and specify or create a new folder in the dialog box.
Individual categories for the attribute must then be entered. Enter a name of the New category in the New category text box and click Add (Figure 11). The Name of the new category will show up in the table. The category can also be edited by clicking or deleted by clicking (visible on mouse-over). Repeat to add additional categories within the attribute.
A waiting task may be waiting for upstream tasks to complete ( ) or waiting for more computing resources to be available ( ).
The Action column contains the cancel button ( ) while a task is queued or running. Clicking this button will cancel the task. A trash icon ( ) will appear in the Action column for completed, canceled or failed tasks, and will allow the task to be deleted from the project. Deleting a task in the Queue tab will remove the corresponding nodes in the Analyses tab. Unless the user has admin privileges, a user may only cancel and delete a task that he/she started. The User, End, and Status columns may be used to filter ( ) the table.
If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.
To add a collaborator, use the Add member drop-down menu. The drop-down menu will list users you are collaborating with on any project on the current instance of Partek Flow. Click a user name in the drop-down list and then click the button to add them as a collaborator. To add a user you have not collaborated with before, type their exact username (e.g., jsmith) and click the button to add them. Depending on the collaborator's preference settings, an email notification may be sent to the email address associated with their user account. To delete a collaborator, select the next to their username (you will be asked for confirmation).
To hide the context sensitive menu, simply click the symbol on the upper left corner of the context sensitive menu. Clicking the triangles will collapse ( ) or expand ( ) the different categories of tasks that are shown.
A verification dialog will appear (Figure 12). A yellow warning sign will show up if there some downstream tasks performed by collaborators will be affected. Deleting the tasks output files optional. If this is not selected, the task nodes will disappear from the Analyses tab but the output files will remain in the project output directory.
Data associated with any data node can be downloaded using the Download data link in the context sensitive menu (Figure 23). Compressed files will be downloaded to the local computer where the user is accessing the Partek Flow server. Note that bigger files (such as unaligned reads) would take longer to download. For guidance, a file size estimate is provided for each data node. These zipped files can easily be imported by the Partek® Genomics Suite® software.
If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.
If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.
A project may be deleted from the Partek Flow server using the button on the upper right side of the Project View page (Figure 1).
Every project can be exported before it is removed from the server. By exporting old projects, you can free up some storage on your server. You can import the exported project back into Partek Flow later if needed.
When you export a project, you will be asked whether to include library files to export or not. If you choose Yes, the current version of library files used in the project will be archived and you can reproduce the result when you later import the project and re-do the analysis. However, it will make the archive size bigger. If you choose No, the library files will not be exported. Note that when you import the project later, you can only use the available version of needed library files to re-do the same analysis, and the results might not be the same.
The Import project option is under Projects drop-down menu on the top of the Partek Flow page (Figure 5). This can be accessed on any Partek Flow page.
The input of this option is the zipped file of the exported project. Browse to the file location which can either be the Partek Flow server, a local machine, or a URL. The zip file first needs to be uploaded to the Partek Flow server (if it is not on the server already), and then Partek Flow will unpack the zip file into a project. The project name will be the same as the exported project name. If the project with the same name already exists, the imported project will have a number appended to it (e.g., ProjectName_1).
The owner of the imported project will be the user that imported it.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
If a project is publicly available in the Gene Expression Omnibus (GEO) and European Nucleotide Archive (ENA) databases, you can import associated FASTQ files, sample attributes, and project details automatically into Partek Flow.
Click Projects at the top of the page
Click Import project
Choose GEO / ENA project for Select files from
Type the BioProject ID or the GEO Accession number
The format of a BioProject ID is PRJNA followed by one to six numbers (e.g., PRJNA291540). The format of a GEO Accession number is GSE followed by one to five numbers (e.g., GSE71578).
Click Import project at the bottom
The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 3). It may take a while for the download to complete depending on the size of the data. FASTQ files are downloaded from the ENA BioProject page.
If the study is not publicly available in both GEO and ENA, project import will not succeed.
If there is an ENA project, but the FASTQ files are not available through ENA, the project will be created, but data will not be imported.
A variety of other issues and irregularities can cause imports to not succeed or partially succeed, including, but not limited to, a BioProject having multiple associated GSE IDs, incomplete information on the GEO or ENA page, and either the GEO or ENA project not being publicly available.
The Gene Expression Omnibus (GEO) and the European Nucleotide Archive (ENA) are web-accessible public repositories for genomic data and experiments. Access and learn more about their resources at their respective websites:
GEO - https://www.ncbi.nlm.nih.gov/geo/
ENA - https://www.ebi.ac.uk/ena
You can search ENA using the GEO ID (e.g., GSE71578) to check if there is a matching ENA project (Figure 6).
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Alternatively, you can also delete your projects directly from the Homepage by clicking Delete project under the Actions column (Figure 2).
After clicking the Delete project, a page displaying all the files associated with the project appears. Clicking the triangle will expand the list. Select the files to be deleted from the server by clicking the corresponding checkboxes next to each file (Figure 3). By default, all output files generated by the project will be deleted.
If you wish to delete the input files associated with the project, you can do that as well by clicking the Input files checkbox. Note that a warning icon appears next to input files that are used in other projects (Figure 4). These cannot be deleted until all projects associated with them are deleted.
Open a project and on the analysis page, click on the gear button and choose Export project (Figure 1). You can also export the project directly from Partek Flow home page by clicking the icon under the Action column (Figure 2).
