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You can review the current library file directory location and privilege settings that determine whether non-administrative users can add or remove library files (Figure 1).

 

 

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SubtitleText System preferences page showing library file directory location and privilege settings. Settings can be changed by clicking on Edit system preferences at the bottom AnchorName sys-preferences

 

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SubtitleText For many model organisms, automatic downloads of gene/feature annotation models from various sources are available from the Partek repository. AnchorName add-annot-model
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If you prefer to add a custom annotation file or if you are working with a custom assembly, choose Add annotation model from the Annotation model drop-down list (Figure 34). You may need to scroll to the bottom of the drop-down list to see this option. Name the annotation model by typing into the Custom Name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 

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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 37)

    

    

    

    

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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
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3. Choose the species and assembly in the the Add Bowtie 2 index dialog dialog. If the species and assembly you want do not appear in the drop-down lists, choose choose Other and  and manually type the names (Figure 38)
4. Choose Choose Whole genome from the  from the Index drop drop-down list (Figure 38)
5. Select the the Build index radio  radio button (Figure 38)Click

6. Click Create (Figure 38)

    

    

    

    

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

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enrichmnt analysis

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 39)
   
   
   

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   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 40), 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 41). 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.

    

    

    

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

Microarray library files can be managed by clicking the Microarray libraries tab on the Library file management page (Figure 42). 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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SubtitleText Manually download microarray probe tab annotation files AnchorName add-probe-seq

To add a custom probe tab file (e.g. for a custom chip), click the green Add probe sequence button at the top of the page (Figure 42, above). Scroll to the bottom of the Chip name drop-down list and choose Other / Custom. Name the chip by typing into the Custom Name box and click the Create button (Figure 44). Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 

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