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SubtitleText Initial setup of library file management performed at the third step of installation AnchorName lfm-install
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Library File Directory

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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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To change where the library files are stored, click Edit system preferences at the bottom and click Browse to point to another directory (Figure 3).

 

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SubtitleText Changing where the library files are stored AnchorName library-file-dir
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You can control whether non administrative users can manage library files. If you only want administrative users to manage library files, click Edit system preferences and select the checkbox shown in Figure 4. Non Administrative users will still be able to view the library files. Unselecting the checkbox will allow any user to manage library files, but only administrative users can remove entire assemblies. The assemblies and library files created by non administrative users will be available for all Partek Flow users.

 

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SubtitleText Change whether administrative or non administrative users can manage library files. AnchorName admis-manage-library-files
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Library File Management Page

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SubtitleText Genomic library files page AnchorName genomic-library-files-page
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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

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

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SubtitleText BWA reference aligner index files for human hg18 assembly AnchorName bwa-library-file-details
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Some of the supported aligners share indexes. If you want to align using Tophat, the Bowtie aligner indexes can be used. If you want to align using Tophat2, the Bowtie2 aligner indexes can be used.

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SubtitleText Annotation models are displayed in separate tables. AnchorName annotation-models
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The gray arrows (/) next to the annotation model name expand/collapse each table. The three annotation models displayed are different versions from the same source (RefSeq), distinguishable by their date. Aligner indexes (e.g. for alignment to the transcriptome) are added to the table of the corresponding annotation model.

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SubtitleText The date and time the library index was last updated is displayed at the bottom of the library file management page. AnchorName ubdate-lib-index
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Creating an Assembly on the Library File Management Page

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SubtitleText Adding an assembly on the library file management page AnchorName add-assembly
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In the Add assembly dialog, choose the Species from the drop-down list (Figure 11), followed by the Assembly version (Figure 12) and click Add. The dialog will automatically load commonly used assembly versions for the selected species (Figure 12). If the assembly version you want does not appear in the list, choose Other and type the custom assembly version name (Figure 13). 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 the chosen species, commonly used assembly versions can be chosen from the drop-down list AnchorName add-assembly-assembly
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SubtitleText A new assembly version can be added by choosing Other and typing the custom assembly version name manually AnchorName add-assembly-other

If the species you want to add does not appear in the list, scroll to the bottom of the species list, choose Other and manually type the species name and assembly version (Figure 14).

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SubtitleText The green plus icon is used to add library files to a section on the library file management page (left). The icon turns gray if all possible library files have been added to a section (right). AnchorName add-file-section
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Alternatively, library files can be added by clicking on the green Add library file button on the library file management page (Figure 16). Choose a library type from the drop-down list in the Add library file dialog (Figure 17) and the dialog will present options specific for each type. If certain library files have already been associated with an assembly, they will not appear as options in the dialogs. For example, if a reference sequence has already been associated with an assembly, it will not appear as an option in the drop-down list shown in Figure 17.

 

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SubtitleText Add library file button on library file management page AnchorName add-lib-file-button

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SubtitleText Add library file dialog AnchorName Add-lib-file-dialog
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All library file tasks are logged in the System queue, which can be accessed by clicking on the avatar in the top right corner, choosing Settings and clicking System queue on the left. When a library file is being created, the hourglass icon ( ) will appear in the Actions column (Figure 5, above). Clicking this icon will display information on the task progress (Figure 18).

 

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SubtitleText Clicking the hourglass icon displays the task progress AnchorName lib-file-progress
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Adding a Reference Sequence

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SubtitleText For custom assemblies, automatic downloads are not available so the reference sequence has to be imported from another source. AnchorName custom-ref
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The Import reference sequence option allows you to add a reference sequence from the Partek Flow Server, My Computer or a URL download link (Figure 21).

 

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SubtitleText A reference sequence can be added from multiple sources AnchorName lib-file-select-file
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To add a reference sequence from the Partek Flow server, select Partek Flow Server, click Browse and navigate to the directory storing the reference sequence file(s) (Figure 22). Only files with the correct file extensions (.fa, .2bit or any compressed format) will be displayed in the file browser. Select the checkbox next to the file name(s) you wish to import and click Continue (Figure 22). Click Finish to add the selected reference sequence file(s) (Figure 21).

 

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SubtitleText Add a reference sequence file(s) from the Partek Flow Server AnchorName add-ref-seq-server
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To upload a reference sequence from your local computer select My computer, click Choose file and navigate to the location of the file(s) on your local machine (Figure 23). It is not advisable to upload large files through the web browser, as this will likely result in an error (e.g. an upload timeout). Administrative users are able to set a limit on the upload file size via System preferences (Figure 2, above). The default file size limit is 500 MB. Please note that only one file can be uploaded at a time. Click Finish to add the selected reference sequence file(s) (Figure 23).

 

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SubtitleText Upload a reference sequence file from your local computer through the browser AnchorName upload-ref-seq
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To download a reference sequence (e.g. from a public repository such as ENSEMBL), select URL and input the URL address (Figure 24). Make sure to include the full URL address, starting with the transfer protocol (e.g. http:// or ftp://) and ending with the file name. It is advisable to find the download link address, copy it to the clipboard and paste it into the Input URL box. Click Finish to add the selected reference sequence file(s) (Figure 24).

 

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SubtitleText Download a reference sequence from the internet AnchorName download-ref-seq
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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.

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SubtitleText For custom assemblies, automatic downloads are not available so the cytoband has to be created AnchorName custom-cytoband
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Adding Reference Aligner Indexes

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SubtitleText For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or imported AnchorName build-index
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Adding a Gene Set

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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
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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 30). Name the gene set by typing into the Custom Name box and click Create. 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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SubtitleText Adding a custom gene set AnchorName adding-custom-gene-set
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Adding a Variant Annotation Database

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SubtitleText For human - hg19, automatic downloads of various variant annotation databases are available from the Partek repository. AnchorName add-variant-annotation-db
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Choose a database from the drop-down list, select the Download variant database radio button and click Create.

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SubtitleText Add a custom variant annotation database AnchorName add-custom-variant-annotation
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Adding a SNPEff Variant Database

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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
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Adding an Annotation Model

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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 35). 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.

 

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SubtitleText Add a custom annotation model AnchorName add-custom-annot-model
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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 36).

 

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SubtitleText When importing an annotation model, the data type must be specified AnchorName import-annot-specify-type
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Adding Aligner Indexes Based on an Annotation Model

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SubtitleText Building an aligner index for an annotation model AnchorName build-aligner-index
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Adding Library Files from Within a Project

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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

3. 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 38)
   
   

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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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4. 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 39)
5. Choose Whole genome from the Index drop-down list (Figure 39)
6. Select the Build index radio button (Figure 39)
7. Click Create (Figure 39)

 

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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 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 40)
   
   

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   SubtitleText If no gene sets are associated with the assembly, click the button to add one. AnchorName create-gene-set
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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 41), 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 42). 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

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SubtitleText Microarray libraries files tab AnchorName microarray-lib-file
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Microarray probe tab files are used for processing microarray data in Partek Flow. When microarray intensity data files (e.g. Affymetrix .CEL files) are imported into a project, the chip type is automatically detected and the appropriate probe tab annotation file is downloaded. Thus, you would normally not need to manually add any probe tab annotation files.

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SubtitleText Manually download microarray probe tab annotation files AnchorName add-probe-seq
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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 43, 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 45).

 

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