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SubtitleText A reference sequence can be added from multiple sources AnchorName lib-file-select-file

To add a reference sequence from the Partek Flow server, select Partek Flow Server, click Browse and navigate to the directory storing the reference sequence file(s) (Figure 22). 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 22). Click Finish to add the selected reference sequence file(s) (Figure 21).

 

 

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SubtitleText Add a reference sequence file(s) from the Partek Flow Server AnchorName add-ref-seq-server

To upload a reference sequence from your local computer select My computer, click Choose file and navigate to the location of the file(s) on your local machine (Figure 23). It is not advisable to upload large files through the web browser, as this will likely result in an error (e.g. an upload timeout). Administrative users are able to set a limit on the upload file size via System preferences (Figure 2, above). The default file size limit is 500 MB. Please note that only one file can be uploaded at a time. Click Finish to add the selected reference sequence file(s) (Figure 23).

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SubtitleText Upload a reference sequence file from your local computer through the browser AnchorName upload-ref-seq

To download a reference sequence (e.g. from a public repository such as ENSEMBL), select URL and input the URL address (Figure 24). 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 24).

 

 

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SubtitleText Download a reference sequence from the internet AnchorName download-ref-seq

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 visa-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.

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1. Under the Analyses tab of a project, select an Unaligned reads data node
2. From the toolbox on the right, choose Aligners followed by Bowtie 2

3. 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 38)
   
   
   

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   SubtitleText The drop-down list will show all assemblies that have a Bowtie 2 index associated with them. Choose New assembly... to add a Bowtie 2 index to another assembly. AnchorName new-lib-file-task

4. 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 Other and manually type the names (Figure 39)
5. Choose Whole genome from the Index drop-down list (Figure 39)
6. Select the Build index radio button (Figure 39)
7. Click Create (Figure 39)

 

 

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SubtitleText Add Bowtie 2 index to another assembly not listed in Figure 38. AnchorName add-other-assembly

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

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