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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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Gene sets. Gene set files are required for biological interpretation analyses (e.g. GO enrichment). Genes are grouped together according to their biological function. Gene set files have to be in GMT format, where each row represents one gene set. The first column of a GMT file is the GO ID or gene set name. The second column is an optional text description. Subsequent columns are the gene symbols that belong to each gene set.
Gene ontologies for various model organisms are available for automatic download from the Partek repository (source: geneontology.org). Because gene ontologies are frequently updated, geneontology.org is 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).
Variant annotations. Variant annotation databases are collections of known genomic variants (e.g. single nucleotide polymorphisms). If you have performed a variant detection study, detected variants can be searched against variant annotation library files to see if the detected variants are known from previous studies. Furthermore, you can validate detected variants against 'gold-standard' variant annotation library files. Variant annotation files are typically in VCF format.
Variant annotation databases from commonly used sources (e.g. dbSNP) are available for automatic download from the Partek repository. Because variant annotation databases 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).
SnpEff variant databases. SnpEff (1) is a variant annotation and effect prediction tool that requires its own variant annotation files, separate to the other Variant annotation library files. If you wish to use SnpEff, library files need to be added to this section.
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Annotation models will appear in separate tables (Figure 7). 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).
Annotation models are used for quantification in gene expression analyses, annotating detected variants (e.g. to predict amino acid changes), visualizations in Chromosome view, generating coverage reports and for aligner index creation (see below). Typical file formats include GTF, GFF, GFF3 and BED.
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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 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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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 below.
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 16, 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 26).
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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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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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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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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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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).
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