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The library files associated with the selected assembly are organized into six major sections (Figure 4, above).

Below is some information on each section. For more detail on adding library files, see the Adding library files to an assembly on the library file management page section of this user guide.

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Cytoband files are used for drawing ideograms of chromosomes in the Chromosome view, including positions of cytogenetic bands if known.

Anchor
Reference-aligner-indexes Reference-aligner-indexes

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 6) 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 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 Adding Aligner Indexes Based on an Annotation Model). Typical file formats include GTF, GFF, GFF3 and BED.

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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 7, 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 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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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 4, above). Clicking this icon will display information on the task progress (Figure 17).

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Adding a Reference Sequence

Click the green plus ( ) icon next to the Reference Files section header (Figure 14, above) 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, 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 18).

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Numbered figure captions
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. AnchorName add-ref-seq

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 18, 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.

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Adding a Cytoband

Click the green plus ( ) icon next to the Reference Files section header (Figure 14, above) 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, 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 24).

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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, seeAdding 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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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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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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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 31). Name the variant annotation database by typing into the Custom Name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 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 16, 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 32).

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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 33). Alternatively, click the Add library file button and choose Gene/feature annotation from the Library type drop-down list (Figure 16, 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 33).

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Numbered figure captions
SubtitleText Add a custom annotation model AnchorName add-custom-annot-model

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).

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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).

Choose the aligner you wish to use from the Aligners drop-down list (Figure 36). All aligners are available for indexing to an annotation model.

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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 42, above). Choose the chip name from the drop-down list in the dialog, select the Download probe sequence radio button and click Create (Figure 43). 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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Numbered figure captions
SubtitleText Manually download microarray probe tab annotation files AnchorName add-probe-seq

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 42, 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 44). Characters such as $ * | \ : " < > ? / % cannot be used in custom names. 

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Numbered figure captions
SubtitleText Adding a custom probe tab file e.g. for a custom microarray chip AnchorName add-custom-probe-seq

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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Adding Aligner Indexes Based on an Annotation Mode