Flow Documentation

Partek Flow Documentation

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Note that this task is for adding indexes for alignment to the whole genome. If you want to align to the transcriptome or another set of genomic features, see Adding Aligner Indexes Based on an Annotation Model.

 

Click the green plus () icon next to Reference aligner indexes section the Gene sets section header. Alternatively Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list and whole genome from the Index to drop-down list. If an aligner index is already associated with an assembly, it will not appear in the Aligner drop-down list. If all but one of the possible aligner indexes have been added, the remaining aligner index will be the only option and will not appear in a drop-down list (Figure 1).

 

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Figure 1. Add aligner index dialog. If more than one aligner index has not been added to an assembly, the missing aligner indexes will appear in the drop-down list (left). If only one aligner index remains to be added, it will be the only option (right). .

If you are using an assembly supported by Partek (e.g. human), a gene set from geneontology.org will appear in the Add gene set drop-down list (Figure 1). Select the Download gene set radio button and click Create.

 

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Alternatively, select Build index and click Create to build the reference aligner index. To build an aligner index, a reference sequence file must already be associated with the assembly. Depending on the aligner, you may have to specify further parameters. Consult the user documentation for each aligner for guidance (usually available on-line).

Alternatively, select Import index and click Create to add an aligner index from another source. An aligner index can be added from the Partek Flow Server, My Computer or a URL download
Figure 1. For many model organisms, automatic downloads of gene sets are available from the Partek repository
 
Choose the aligner index you wish to add from the drop-down list in the Add aligner index dialog (Figure 1). The following indexes can be added:
  • Bowtie
  • Bowtie colorspace
  • Bowtie 2
  • TMAP
  • BWA
  • SHRiMP 2
  • SHRiMP 2 colorspace
  • Issac 2
  • STAR
  • STAR 2.4 1d
  • GSNAP
  • GSNAP v8
If you are using an assembly supported by Partek (e.g. human), there are three radio button options: Download index; Build index or Import index (Figure 1). Certain aligner indexes may not be available for automatic download because the file sizes are too large to download efficiently.

If available, select Download index and click Create to get the chosen reference aligner index from the Partek repository.

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 2). Name the gene set by typing into the Custom Name box and click Create. 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). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible . This will vary for each aligner.For custom assemblies (e.g. for non-model organisms), only the Build index and Import index options are available (Figure 2).gmt and various compressed formats).

 

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Figure 2. For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or importedAdding a custom gene set

 

Additional assistance

 

 

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