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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)

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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