Adding Aligner Indexes Based on an Annotation Model
Last updated
Last updated
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.
On the library file management page, click the + Add annotation models button at the Annotation models section and choose Aligner index from the Library type drop-down list in the dialog (Figure 1).
Choose the aligner you wish to use from the Aligner drop-down list (Figure 1). All 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 1). To build an aligner index based on an annotation model, a reference sequence file must already be associated with the assembly.
If you are using an assembly supported by Partek (e.g. human), annotation models from a variety of commonly used sources will appear in the Index to drop-down list in addition to the ones that have already been associated with the assembly. If you choose an annotation model that has not already been associated, it will automatically be downloaded prior to building the index.
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