# Importing aligned reads

We will be using the *RNA-Seq* workflow to analyze RNA-Seq data throughout this tutorial. The commands included in the *RNA-Seq* workflow are also available form the command toolbar, but may be labeled differently.

* Select the *RNA-Seq* workflow by selecting it from the *Workflow* drop-down menu in the upper right-hand corner of the Partek Genomics Suite window (Figure 1)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c871a756b5750acd33eff309c8eb465a21b17e1a%2F2017-08-07%2015_02_51-Partek%20Genomics%20Suite.png?alt=media)

Figure 1. Selecting the RNA-seq workflow

The Partek Genomics Suite software can import next generation sequencing data that has been aligned to a reference genome. Two standard types of alignment formats can be imported: .BAM and .SAM. It is also possible to concert ELAND .txt files to .BAM files with the converter found in the *Tools* menu in the main command bar. The data used in this tutorial was aligned using the Partek® Flow® software and saved as .BAM files.

* To import the .BAM files, select **Import and Manage Samples** from the *Import* section of the *RNA-Seq* workflow. The *Sequence Import* dialog box will open (Figure 2)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-14510978ac1a22650f488237e421a14cd8af966d%2Ffig2.png?alt=media)

Figure 2. Importing .BAM files

* Select *BAM Files (\*.bam)* from the *Files of type* drop-down menu if not set by default
* Use the file browser panel on the left-hand side of the *Sequence Dialog* or select **Browse...** to navigate to the folder where you stored the tutorial .BAM files
* Files with checked boxes next to the file name will be imported. For this tutorial, select **brain\_fa**, **heart\_fa**, **liver\_fa**, and **muscle.fa**
* Select **OK** to confirm the file selection and open the next dialog (Figure 3)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d84fb167e21b0c1e7d64aa080f8559c8af871f71%2Ffig3.png?alt=media)

Figure 3. Viewing the Sequence Import wizard; specify Output file (and directory using Browse), Species, and Genome

* Configure the dialog as shown (Figure 3)

*Output file* provides a name for the top-level spreadsheet. **Browse** can be used to change the output directory.

* Select **Homo sapiens** from the *Species* drop-down menu

This will allow us to select a human genome reference assembly alignment.

* Select **hg19** for *Genome/Transcriptome reference used to align the reads*

This is the reference genome our tutorial data was aligned to using Partek Flow.

* Select **OK** to open the *BAM Sample Manager* dialog (Figure 4)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2b478dd93d67f03222bab030e205772a430456d0%2Ffig4.png?alt=media)

Figure 4. Bam Sample Manager dialog

The *Bam Sample Manager* dialog allows additional samples to be added or removed after the initial sample import. To remove a sample, select a sample from the list and then select **Remove selected samples**. This dialog also allows us to modify samples.

* Select **Manage samples** to open the *Assign files to samples* dialog

*Sample ID* is by default set to the file name, which may be too long or uninformative, so the *Assign files to samples* dialog can be used to give informative names to samples.

* Change the samples names to *Brain, Heart, Liver,* and *Muscle* as shown (Figure 5)

The *Assign files to samples* dialog also allows multiple .BAM files to be merged into one sample. This is useful if reads from one sample are split into multiple .BAM files.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-782c4d6e06af5a723df4391b7aff1288b1a6b9ec%2Ffig5.png?alt=media)

Figure 5. Changing sample names using the Assign files to samples dialog

* Select **OK** to close the **Assign files to samples** dialog
* Select **Close** to exit the *Bam Sample Manager* dialog and view the imported data (Figure 6)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a927271894bb88fb5e5fb6167a4fea5b8fb6ddc0%2Ffig6.png?alt=media)

Figure 6. Viewing the imported data in a spreadsheet

Additional files can be added to this spreadsheet using the *Bam Sample Manager* dialog. The *Bam Sample Manager* dialog can also be used to add imported samples to a separate spreadsheet by selecting a new option in the dialog, **Add new experiment**.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.