How do you create a multiple reference genome in Hisat2?
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5 months ago
Aaron • 0

I need to combine two separate reference genomes into one index, so that I can align my sequencing files to one assembly. Is there a way to do this in Hisat2? I need to be able to index them as one index and not multiple indices. Only used Hisat2 for aligning to single genomes, not experienced with creating custom genomes like this!

hisat2 alignment RNA-Seq next-gen assembly • 227 views
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What did you try? Did you try making one large fasta with both genomes and indexing that?

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I haven't, no. This is what I'm trying to do. Do I build the fasta using HIsat2? I would need to do the same for the annotations also.

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No, just use cat to combine things, though you may have to see if your annotation files has headers. You will probably want to use sed or something to make sure the chromosome names are different between your two references, if they aren't already.

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