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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.
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Library File Management Page
To access the library file management page click the avatar in the top right corner and choose Settings. Then click Library file management on the left.
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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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Library Files
The library files associated with the selected assembly are organized into six major sections (Figure 4).
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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). The aligner indexes generated will be added to the corresponding annotation model table (Figure 7).
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. To check for recent updates, click here.
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Creating an Assembly on the Library File Management Page
On the library file management page, an assembly can be added by choosing Add assembly… from the Assembly drop-down list (Figure 9). If the list is long, you may need to scroll to the bottom.
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Adding Library Files on the Library File Management Page
Library files can be added to an assembly by clicking the green plus () icon next to the header of each section (Figure 14) 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 14).
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Adding a Reference Sequence
Click the green plus () icon next to the Reference Files section header (Figure 14) 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). 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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Adding a Cytoband
Click the green plus () icon next to the Reference Files section header (Figure 14) 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). 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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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.
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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).
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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).
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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).
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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).
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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.
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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)
- Under the Analyses tab of a project, select an Unaligned reads data node
From the context sensitive menu 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 37)
Numbered figure captions 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 - 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 38)
- Choose Whole genome from the Index drop-down list (Figure 38)
- Select the Build index radio button (Figure 38)
Click Create (Figure 38)
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 enrichmnt 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 39)
Numbered figure captions SubtitleText If no gene sets are associated with the assembly, click the button to add one. AnchorName create-gene-set 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). Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 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.
Numbered figure captions SubtitleText Download a gene set using the Create gene set dialog from within a project AnchorName select-gene-set Numbered figure captions SubtitleText Import a gene set using the Create gene set dialog from within a project AnchorName custom-gene-set-task
Microarray Library Files
Microarray library files can be managed by clicking the Microarray libraries tab on the Library file management page (Figure 42). The chip name and download source of stored Microarray library files are shown in the table. For more information, refer to the Microarray Toolkit section.
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Quick Video Demo of Library File Management
The short clip below (video only, no audio) shows how to quickly setup some library files for the hg19 human reference genome assembly. The process can be adapted to the different kinds of file types.
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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