Question: How do you create a multiple reference genome in Hisat2?
gravatar for Aaron
21 days ago by
Aaron0 wrote:

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!

ADD COMMENTlink written 21 days ago by Aaron0

What did you try? Did you try making one large fasta with both genomes and indexing that?

ADD REPLYlink written 21 days ago by swbarnes29.4k

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.

ADD REPLYlink written 21 days ago by Aaron0

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.

ADD REPLYlink written 21 days ago by swbarnes29.4k
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