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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 36). 

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Click the green plus () icon next to the Annotation models section header and choose Aligner index from the Library type drop-down list in the dialog (Figure 3637). Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 16).

Choose the aligner you wish to use from the Aligners drop-down list (Figure 3637). 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 3637). To build an aligner index based on an annotation model, a reference sequence file must already be associated with the assembly.

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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 3738)

    

    

    

    

   Numbered figure captions
   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

    

    

    

3. 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 3839)
4. Choose Whole genome from the Index drop-down list (Figure 3839)
5. Select the Build index radio button (Figure 3839)

6. Click Create (Figure 3839)

    

    

    

    

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

    

    

    

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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 Enrichment analysis

3. If there are no gene set files associated with the relevant assembly, click Create gene set (Figure 3940)
   
   
   

   Numbered figure captions
   SubtitleText If no gene sets are associated with the assembly, click the button to add one. AnchorName create-gene-set

4. If you are working with an assembly/species supported by Partek (e.g. human), choose a gene set from the Create gene set drop-down list (Figure 4041), select the Download gene set radio button and select Create. Alternatively, choose Add gene ontology source from the Create gene set drop-down list, manually type the custom gene set name and click Create to import your own gene set from the Partek Flow server, My computer or URL (Figure 4142). 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.

    

    

    

   Numbered figure captions
   SubtitleText Download a gene set using the Create gene set dialog from within a project AnchorName select-gene-set

    

    

   
   
   

   Numbered figure captions
   SubtitleText Import a gene set using the Create gene set dialog from within a project AnchorName custom-gene-set-task

    

    

    

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Microarray library files can be managed by clicking the Microarray libraries tab on the Library file management page (Figure 4243). The chip name and download source of stored Microarray library files are shown in the table. For more information, refer to the Microarray Toolkit section.

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To manually download a probe tab file, click the green Add probe sequence button at the top of the page (Figure 4243). Choose the chip name from the drop-down list in the dialog, select the Download probe sequence radio button and click Create (Figure 4344). If a chip has already been added, it will not appear in the Chip name drop-down list. We currently support automatic downloads of a broad variety of Affymetrix and Illumina microarray chips.

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