The library file management tool in
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Partek® Flow® provides an easy way to create, process and manage reference sequences, cytoband files, annotation models, aligner indexes, gene sets, variant databases and microarray probe sequence files.
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Initial Setup of Library Files During Installation
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| SubtitleText | Initial setup of library file management performed at the third step of installation |
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| AnchorName | lfm-install |
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Library File Directory
The specified directory will store the library files. 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
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 2).
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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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| SubtitleText | Changing where the library files are stored |
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| AnchorName | library-file-dir |
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| SubtitleText | Change whether administrative or non administrative users can manage library files. |
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| AnchorName | admis-manage-library-files |
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Library File Management Page
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| SubtitleText | Genomic library files page |
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| AnchorName | genomic-library-files-page |
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Selecting an Assembly
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| SubtitleText | Human assembly versions hg17, hg18 and hg19 will appear as separate assemblies in the drop-down list. |
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| AnchorName | human-assembly-versions |
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Library Files
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| SubtitleText | BWA reference aligner index files for human hg18 assembly |
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| AnchorName | bwa-library-file-details |
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| SubtitleText | Annotation models are displayed in separate tables. |
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| AnchorName | annotation-models |
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The gray arrows (Image Removed/Image Removed) 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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Update Library Index
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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. |
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| AnchorName | ubdate-lib-index |
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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 10). 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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| SubtitleText | Add assembly dialog. The species can be chosen from the drop-down list |
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| 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 |
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| 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 |
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| AnchorName | add-assembly-other |
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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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Adding Library Files on the Library File Management Page
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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 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 |
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| AnchorName | add-lib-file-button |
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| SubtitleText | Add library file dialog |
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| AnchorName | Add-lib-file-dialog |
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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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Adding a Reference Sequence
Click the green plus ( Image Removed ) icon next to the Reference Files section header (Figure 15, above) and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 19). Alternatively, click the Add library file button and choose Reference sequence from the Library type drop-down list (Figure 17, 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 19).
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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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| 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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| SubtitleText | A reference sequence can be added from multiple sources |
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| AnchorName | lib-file-select-file |
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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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| 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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| SubtitleText | Download a reference sequence from the internet |
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| AnchorName | download-ref-seq |
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Adding a Cytoband
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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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| 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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| 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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- Bowtie
- Bowtie colorspace
- Bowtie 2
- TMAP
- BWA
- SHRiMP 2
- SHRiMP 2 colorspace
- Issac 2
- STAR
- STAR 2.4 1d
- GSNAP
- GSNAP v8
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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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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/) |
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| AnchorName | add-gene-set |
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| SubtitleText | Adding a custom gene set |
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| AnchorName | adding-custom-gene-set |
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Adding a Variant Annotation Database
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- dbSNP
- Kaviar
- NHLBI Variant Server
- 1000 Genomes
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| SubtitleText | For human - hg19, automatic downloads of various variant annotation databases are available from the Partek repository. |
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| AnchorName | add-variant-annotation-db |
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| SubtitleText | Add a custom variant annotation database |
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| 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. |
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| 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. |
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| AnchorName | add-annot-model |
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| SubtitleText | Add a custom annotation model |
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| AnchorName | add-custom-annot-model |
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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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Adding Aligner Indexes Based on an Annotation Model
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| SubtitleText | Building an aligner index for an annotation model |
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| AnchorName | build-aligner-index |
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Adding Library Files from Within a Project
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)
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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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| 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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| 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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| SubtitleText | Download a gene set using the Create gene set dialog from within a project |
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| AnchorName | select-gene-set |
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| SubtitleText | Import a gene set using the Create gene set dialog from within a project |
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| AnchorName | custom-gene-set-task |
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Microarray Library Files
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| SubtitleText | Microarray libraries files tab |
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| AnchorName | microarray-lib-file |
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| SubtitleText | Manually download microarray probe tab annotation files |
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| AnchorName | add-probe-seq |
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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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References
- Cingolani P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 6(2):80-92. PMID: 22728672
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For a quick start, please watch the short videos below:
Quickly setup library files for the hg19 human reference genome assembly.
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| name | LibraryFiles.mp4 |
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The process can be adapted to the different kinds of file types.
Adding library files for a non-model organism
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| name | How_to_add_library_files_for_non_model_organisms.mp4 |
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| height | 280 |
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You can watch the full webinar on our website.
This user guide will cover the following topics: