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Table of Contents
maxLevel 2 minLevel 2 exclude Additional Assistance

Library File Directory

During the installation of Partek Flow, the library file directory is selected.  Partek Flow needs to have read and write privileges to this directory and the directory should be located on a drive with sufficient storage capacity. For instance, Bowtie index files for the hg19 human reference genome are approximately 3 GB and STAR index files are approximately 15 GB. In addition, the binary .2bit file containing the hg19 reference genome, is just under 800 MB. For more information, refer to  Launching Partek Flow for the First Time.

Library File Management Settings

 

To review and edit library file management settings, you must be logged into Partek Flow as a user with administrator privileges. Click on the avatar in the top right corner and choose Settings. Then click System preferences on the left. 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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Numbered figure captions
SubtitleText Genomic library files page AnchorName genomic-library-files-page

The gray arrows (/) expand/collapse each section. Associated library files are shown in a table in each section. The view file () icon in the Actions column of each table displays additional library file details. The red cross () dissociates a library file. The hourglass () icon indicates a library file is being created

Selecting an Assembly

Choosing an Assembly from the drop-down list at the top will display the associated library files in the pane below. Assemblies are named by the species and the build version (e.g. Homo sapiens (human) - hg19). Different build versions for the same species are regarded as separate assemblies (Figure 5). Administrative users can delete a selected assembly by clicking the red cross ( ).

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Numbered figure captions
SubtitleText Human assembly versions hg17, hg18 and hg19 will appear as separate assemblies in the drop-down list. AnchorName human-assembly-versions

Library Files

The library files associated with the selected assembly are organized into six major sections (Figure 5, above).

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The aligner indexes in the Annotation models section are required if you wish to align to a subset of the genome as defined by the annotation model, e.g. target amplicons or the transcriptome. The reference sequence is still required to generate an aligner index for an annotation model. As with whole genome alignment, indexes are aligner specific, although some aligners share indexes and are version specific (see Reference aligner indexes above). The aligner indexes generated will be added to the corresponding annotation model table (Figure 7, above).

Update Library Index

The library index is a file that contains download sources for all Partek distributed library files. An automatic update of this file will occur every 24 hours (Figure 8), so this normally doesn't require any attention. If you do wish to manually update the library index, click Update Library Index at the bottom of the library file management page.

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Numbered figure captions
SubtitleText Clicking the hourglass icon displays the task progress AnchorName lib-file-progress

Adding a Reference Sequence

Click the green plus ( ) icon next to the Reference Files section header (Figure 14, above) and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 18). Alternatively, click the Add library file button and choose Reference sequence from the Library type drop-down list (Figure 16, above). If a cytoband file is already associated with an assembly, Reference sequence will be the only option available in the Add reference sequence dialog and will not appear in a drop-down list (Figure 18).

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Numbered figure captions
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.

Adding a Cytoband

Click the green plus ( ) icon next to the Reference Files section header (Figure 14, above) and choose Cytoband from the Library type drop-down list in the Add reference sequence dialog (Figure 24). Alternatively, click the Add library file button and choose Cytoband from the Library type drop-down list (Figure 16, above). If a reference sequence is already associated with an assembly, Cytoband will be the only option available in the Add genome dialog and will not appear in a drop-down list (Figure 24).

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Numbered figure captions
SubtitleText For custom assemblies, automatic downloads are not available so the cytoband has to be created AnchorName custom-cytoband

Adding Reference Aligner Indexes

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 below.

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Numbered figure captions
SubtitleText For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or imported AnchorName build-index

Adding a Gene Set

Click the green plus ( ) icon next to the Gene sets section header. Alternatively, click the Add library file button and choose Gene set from the Library type drop-down list (Figure 16, above).
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 28). Select the Download gene set radio button and click Create.

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Numbered figure captions
SubtitleText Adding a custom gene set AnchorName adding-custom-gene-set

Adding a Variant Annotation Database

Click the green plus ( ) icon next to the Variant annotations section header. Alternatively, click the Add library file button and choose Variant annotations from the Library type drop-down list (Figure 16, above)
If you are using a human - hg19 assembly, variant annotation databases from various sources will appear in the Variant annotation drop-down list (Figure 30). Available variant annotation database sources include:

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Numbered figure captions
SubtitleText Add a custom variant annotation database AnchorName add-custom-variant-annotation

Adding a SNPEff Variant Database

Click the green plus ( ) icon next to the SNPEff variant databases section header. Alternatively, click the Add library file button and choose SNPEff variant database from the Library type drop-down list (Figure 16, above).

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Numbered figure captions
SubtitleText Various versions of SNPEff variant databases are available for automatic download. The drop-down list shows databases available for human - hg19 Choose a SNPEff database from the drop-down list, select the Download SNPEff variant database radio button and click Create. AnchorName add-snpeff-db

Adding an Annotation Model

Click the green plus ( ) icon next to the Annotation models section header and choose Gene/feature annotation from the Library type drop-down list in the dialog (Figure 33). Alternatively, click the Add library file button and choose Gene/feature annotation from the Library type drop-down list (Figure 16, above).

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Numbered figure captions
SubtitleText When importing an annotation model, the data type must be specified AnchorName import-annot-specify-type

Adding Aligner Indexes Based on an Annotation Model

Note that this task is for adding indexes for alignment to a subset of the genome (e.g. the transcriptome). If you want to align to the whole genome, see Adding Reference Aligner Indexes above.

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Missing library files can be added when setting up tasks within a project, without having to navigate to the library file management page. The user interface will vary depending on the task and which library files already exist on your system. Below are two examples scenarios.

Adding a missing whole genome aligner index (Bowtie 2 in this example)

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

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Numbered figure captions
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

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)
   
   
   

   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 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 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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