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Library File Directory
During the installation of Partek Flow, a basic setup of library files can be performed (Figure 1). For more information, refer to the Partek Flow installation guide. | Numbered figure captions |
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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
The specified directory will store the library files. Partek 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.
Assemblies
For convenience, commonly used assemblies (e.g. human, mouse, rat) can be added during installation. Their reference genomes, cytobands and most popular annotation files will be downloaded automatically. An assembly can be removed by selecting the red cross ( Image Removed ) icon to the right of the species name (Figure 1, above). Assemblies can be added by clicking Add Assembly. New assemblies can also be added at a later stage (see Creating an assembly on the library file management page).
Reference Aligner Indexes
Pre-built aligner indexes for the selected assemblies can also be downloaded during installation. To include an aligner index, select the checkbox next to the aligner name. For some aligners, e.g. STAR and GSNAP, index files are not available for download. Any missing indexes can be easily built after installation (see Adding Library Files on the Library File Management Page and Adding Library Files from Within a Project).
Further Changes after Installation
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 21).
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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 |
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| 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
32).
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| SubtitleText | Changing where the library files are stored |
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| 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
43. 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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The library file management page has two tabs - Genomic library files and Microarray library files. This section of the user guide will focus on the Genomic library files tab, which is relevant for next-generation sequencing analysis (Figure 54).
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| SubtitleText | Genomic library files page |
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| 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...
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 65). Administrative users can delete a selected assembly by clicking the red cross ( ).
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Reference aligner indexes. Next-generation sequencing aligners require the reference sequence to be indexed prior to alignment, as this greatly increases alignment speed. An index consists of a set of files (Figure 76) and are generally aligner specific. For example, if you wish to align using BWA, you need a BWA index.
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Annotation models will appear in separate tables (Figure 87). If you have multiple versions of annotation models from the same source, it is advisable to distinguish them by their date or version number.
Annotation models from commonly used sources (e.g. Refseq, ENSEMBL) are available for automatic download from the Partek repository. Because annotation models are frequently updated, these sources are checked for updates quarterly. You can check for recent updates to the Partek repository on the Partek website (http://www.partek.com/library-files-updates).
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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 87, 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 98), 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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On the library file management page, an assembly can be added by choosing Add assembly… from the Assembly drop-down list (Figure 109). If the list is long, you may need to scroll to the bottom.
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| SubtitleText | Adding an assembly on the library file management page |
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| AnchorName | add-assembly |
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In the
Add assembly dialog, choose the
Species from the drop-down list (Figure
1110), followed by the
Assembly version (Figure
1211) and click
Add. The dialog will automatically load commonly used assembly versions for the selected species (Figure
1211). If the assembly version you want does not appear in the list, choose
Other and type the custom assembly version name (Figure
1312). 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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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 1413).
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| SubtitleText | A new species can be added by typing the name and assembly name manually |
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| AnchorName | add-assembly-other-species |
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Library files can be added to an assembly by clicking the green plus ( ) icon next to the header of each section (Figure 1514) on the library file management page. This will open a dialog specific to the chosen section. If all possible library files are already associated in each section, the green plus icon will appear gray (Figure 1514).
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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). |
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| 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
1615). Choose a
library type from the drop-down list in the
Add library file dialog (Figure
1716) 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
1716.
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| SubtitleText | Add library file button on library file management page |
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| AnchorName | add-lib-file-button |
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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 54, above). Clicking this icon will display information on the task progress (Figure 1817).
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| SubtitleText | Clicking the hourglass icon displays the task progress |
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| AnchorName | lib-file-progress |
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Click the green plus ( ) icon next to the Reference Files section header (Figure 1514, above) and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 1918). Alternatively, click the Add library file button and choose Reference sequence from the Library type drop-down list (Figure 1716, 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 1918).
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| SubtitleText | Add reference sequence dialog. If the reference sequence and cytoband files have not been added yet, both options will appear in the Library type drop-down list (left). If one is missing, it will appear as the only option (right). For many model organisms, automatic downloads are available from the Partek repository. |
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| AnchorName | add-ref-seq |
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If you are using an assembly supported by Partek (e.g. human), there are two radio button options:
Download reference sequence and
Import reference sequence (Figure
1918, above). Select
Download reference sequence and click
Create to get the reference sequence from the Partek repository. Alternatively, select
Import reference sequence and click
Create to add the reference sequence from another source.
If you are using a custom assembly (e.g. for a non-model organism), only the
Import reference sequence radio button will be available (Figure
2019).
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| SubtitleText | For custom assemblies, automatic downloads are not available so the reference sequence has to be imported from another source. |
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| 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
2120).
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| SubtitleText | A reference sequence can be added from multiple sources |
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| 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
2221). 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
2221). Click
Finish to add the selected reference sequence file(s) (Figure
2120).
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| SubtitleText | Add a reference sequence file(s) from the Partek Flow Server |
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| 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
2322). 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
21, 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
2322).
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| SubtitleText | Upload a reference sequence file from your local computer through the browser |
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| 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
2423). 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
2423).
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| SubtitleText | Download a reference sequence from the internet |
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| 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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Click the green plus ( ) icon next to the Reference Files section header (Figure 1514, above) and choose Cytoband from the Library type drop-down list in the Add reference sequence dialog (Figure 2524). Alternatively, click the Add library file button and choose Cytoband from the Library type drop-down list (Figure 1716, 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 2524).
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| SubtitleText | Add reference sequence dialog. If the reference sequence and cytoband files have not been added yet, both options will appear in the Library type drop-down list (left). If one is missing, it will appear as the only option (right). For many model organisms, automatic downloads are available from the Partek repository. |
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| AnchorName | add-cytoband |
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If you are using an assembly supported by Partek (e.g. human), there are two radio button options:
Download cytoband and
Create cytoband from 2bit (Figure
2524). Select
Download cytoband and click
Create to get the cytoband file from the Partek repository. Alternatively, select
Create cytoband from 2bit and click
Create to build the cytoband file. If the reference sequence is missing, it will either be downloaded automatically or you will be asked to import it from another source (see
Adding a reference sequence).
If you are using a custom assembly (e.g. for a non-model organism), only the Create cytoband from 2bit option is available (Figure 2625).
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| SubtitleText | For custom assemblies, automatic downloads are not available so the cytoband has to be created |
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| AnchorName | custom-cytoband |
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Click the green plus ( ) icon next to the Reference aligner indexes section header. Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 1716, above) 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 2726).
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| SubtitleText | 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). For many model organisms, automatic downloads are available from the Partek repository. |
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| AnchorName | add-aligner-index-dialog |
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Choose the aligner index you wish to add from the drop-down list in the
Add aligner index dialog (Figure 27). The following indexes can be added:
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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 2726). Certain aligner indexes may not be available for automatic download because the file sizes are too large to download efficiently.
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For custom assemblies (e.g. for non-model organisms), only the Build index and Import index options are available (Figure 2827).
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| SubtitleText | For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or imported |
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| AnchorName | build-index |
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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 1716, 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 2928). Select the Download gene set radio button and click Create.
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| SubtitleText | For many model organisms, automatic downloads of gene sets are available from the Partek repository (source: http://geneontology.org/) |
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| 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
3029). 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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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 1716, 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 3130). Available variant annotation database sources include:
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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 3231). Name the variant annotation database by typing into the Custom Name box and click Create. 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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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 1716, above).
If you are using human (hg19 and hg38), mouse (mm10) or rat (rn5 and rn6) assemblies, various versions of SNPEff variant databases are available for automatic download (Figure 3332).
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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. |
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| AnchorName | add-snpeff-db |
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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 3433). Alternatively, click the Add library file button and choose Gene/feature annotation from the Library type drop-down list (Figure 1716, above).
If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources (e.g. RefSeq, ENSEMBL, GENCODE) will appear in the Annotation model drop-down list in the dialog. Choose an annotation model, select the Download annotation file radio button and click Create (Figure 3433).
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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. |
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| 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
3534). 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 |
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| 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
3635).
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| SubtitleText | When importing an annotation model, the data type must be specified |
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| AnchorName | import-annot-specify-type |
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Click the green plus ( ) icon next to the Annotation models section header and choose Aligner index from the Library type drop-down list in the dialog (Figure 3736). Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 1716, above).
Choose the aligner you wish to use from the Aligners drop-down list (Figure 3736). All 10 aligners are available for indexing to an annotation model.
The annotation model(s) that have already been associated with an assembly will appear at the top of the Index to drop-down list. Choose the annotation model you wish to index to, select the Build index radio button and click Create (Figure 3736). To build an aligner index based on an annotation model, a reference sequence file must already be associated with the assembly.
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- Under the Analyses tab of a project, select an Unaligned reads data node
- From the toolbox 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
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36)
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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. |
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| AnchorName | new-lib-file-task |
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- 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)
- Choose Whole genome from the Index drop-down list (Figure 3938)
- Select the Build index radio button (Figure 3938)
- Click Create (Figure 3938)
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| SubtitleText | Add Bowtie 2 index to another assembly not listed in Figure 38. |
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| 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- Under the Analyses tab of a project, select a Feature list data node
- Choose Biological interpretation from the menu on the right, followed by Enrichment analysis
If there are no gene set files associated with the relevant assembly, click Create gene set (Figure 4039)
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| SubtitleText | If no gene sets are associated with the assembly, click the button to add one. |
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| AnchorName | create-gene-set |
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- 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 4140), 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 4241). 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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Microarray library files can be managed by clicking the Microarray libraries tab on the Library file management page (Figure 4342). The chip name and download source of stored Microarray library files are shown in the table.
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To manually download a probe tab file, click the green Add probe sequence button at the top of the page (Figure 4342, above). Choose the chip name from the drop-down list in the dialog, select the Download probe sequence radio button and click Create (Figure 4443). If a chip has already been added, it will not appear in the Chip name drop-down list. We currently support automatic downloads of a broad variety of Affymetrix and Illumina microarray chips.
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| SubtitleText | Manually download microarray probe tab annotation files |
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| 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
4342, 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
4544).
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| SubtitleText | Adding a custom probe tab file e.g. for a custom microarray chip |
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| 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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