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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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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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| 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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| 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
2726). The following indexes can be added:
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Alternatively, select Import index and click Create to add an aligner index from another source. An aligner index 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. This will vary for each aligner.
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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
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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| 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 29). Name the gene set by typing into the
Custom Name box and click
Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 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 |
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| AnchorName | adding-custom-gene-set |
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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, 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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Multiple versions of the above databases are available. For human - hg38, only dbSNP is currently available. This list is periodically updated.
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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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Choose a database from the drop-down list, select the
Download variant database radio button and click
Create.
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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, above).
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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
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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| 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 35).
Choose mRNA for whole transcriptome annotations, where gene and transcript level information is present. Choose microRNA for precursor or mature microRNA transcript annotations. Choose Amplicon for targeted amplicon sequencing annotations. Choose Other for annotation files that do not fall into the other three categories (e.g. lncRNA).
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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
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.
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 36). Alternatively, click the Add library file button, choose Aligner index from the Library type drop-down list (Figure 16, above).
Choose the aligner you wish to use from the Aligners drop-down list (Figure 36). 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 36). 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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| 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
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