# 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)

![](/files/1XeoOpHap1pyKP9eaDDf)

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)

![](/files/2mYqIu9URVhSTR6bsMcV)

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)

![](/files/vKCakmZAGw7wbT73W2S3)

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)

![](/files/srAQUR67gJcqB0A1O2Dm)

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.

![](/files/5EvFIgrWr5iG9H8xxTTq)

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)

![](/files/eub9svP1Z8u7MfKKADHF)

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.


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