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SubtitleText Adding an assembly on the library file management page AnchorName add-assembly

In the Add assembly dialog, choose the Species from the drop-down list (Figure 10), followed by the Assembly version (Figure 11) and click Add. The dialog will automatically load commonly used assembly versions for the selected species (Figure 11). If the assembly version you want does not appear in the list, choose Other and type the custom assembly version name (Figure 12). Note Characters such as $ * | \ : " < > ? / % cannot be used in custom names. Note that If an assembly version for a given species already exists on your system, it will not appear in the drop down list.

 

 

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SubtitleText Add assembly dialog. The species can be chosen from the drop-down list AnchorName add-assembly-species

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SubtitleText For many model organisms, automatic downloads of gene sets are available from the Partek repository (source: http://geneontology.org/) AnchorName add-gene-set

If you prefer to add a custom gene set, or if you are working with a custom assembly, choose Add gene ontology source from the Add gene set drop-down list (Figure 29). Name the gene set by typing into the Custom Name box and click Create. A Characters such as $ * | \ : " < > ? / % cannot be used in custom names. A gene set file can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gmt and various compressed formats).

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If you prefer to add a custom variant annotation database, perhaps from another source or 'gold-standard' validated variants, choose Add variant database from the Variant annotation drop-down list (Figure 31). Name the variant annotation database by typing into the Custom Name box and click Create. A Characters such as $ * | \ : " < > ? / % cannot be used in custom names. A variant annotation database can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.vcf and various compressed formats).

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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

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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SubtitleText Add a custom annotation model AnchorName add-custom-annot-model

A custom annotation model can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.gtf, .gff, .gff3, .bed, .pannot and various compressed formats). You must specify the type of annotation file by choosing an option from the Annotation data type drop-down list (Figure 35).

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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 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). If 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 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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SubtitleText Adding a custom probe tab file e.g. for a custom microarray chip AnchorName add-custom-probe-seq

A custom probe tab file can be added from the Partek Flow Server, My Computer or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a reference sequence, above). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.probe_tab and various compressed formats). Please see the Importing Custom CEL files user guide for more information.

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