HISAT2 relaxing parameters?
Hi,
It’s my first time using HISAT2 and the options have gotten me all confused. How can I run HISAT2 such that I increase the number of mapped reads by relaxing the parameters? Essentially, how can I increase the number of mismatches, etc allowed (which options do I need to use and how)?
Thanks so much!
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In case someone is searching this topic and coming up with nothing: you can increase the number of reads deemed “aligned” by changing the min score from the default (L,0,-0.2) to e.g. (L,0,-0.6) with --score-min L,0,-0.6
. If there are reads that are close enough to the reference, this will result in them being reported as mapped.
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