Hisat2 mapping stringency

Question

[MA]

Dear all, I am running hisat2 with default settings in genomic mapping analysis. I want to run hisat2 with more strict parameters to avoid mismatched reads. Does anyone provide me some suggestions on setting relavent hisat2 options? Thank you very much!

Answer 1

[rfran010]

You can adjust this parameter:

Scoring:
  --mp <int>,<int>   max and min penalties for mismatch; lower qual = lower penalty <6,2>
  --sp <int>,<int>   max and min penalties for soft-clipping; lower qual = lower penalty <2,1>

I would suggest a parameter sweep where you run multiple tests with different values to see how it affects mapping.

One consideration too is that hisat2 is soft-clipping reads, so you may want consider adjusting those options as well, You can see the scoring option above. There's also an option to disable soft-clipping entirely..

[MA]

Thanks a lot! The answer is really helpful!