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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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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).

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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1. Under the Analyses tab of a project, select an Unaligned reads data node
2. 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)
 

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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
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1. 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)
2. Choose Whole genome from the Index drop-down list (Figure 38)
3. Select the Build index radio button (Figure 38)
4. Click Create (Figure 38)

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SubtitleText Microarray libraries files tab AnchorName microarray-lib-file
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Microarray probe tab files are used for processing microarray data in Partek Flow. When microarray intensity data files (e.g. Affymetrix .CEL files) are imported into a project, the chip type is automatically detected and the appropriate probe tab annotation file is downloaded. Thus, you would normally not need to manually add any probe tab annotation files.

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