Is it necessary to include --known-splicesite-infile in HISAT2?

Question

[biolab]

Hi, everyone,

I am using HISAT2 for genomic mapping. In building index, I included --ss and --exon options, which store splicing site information. Then, is it necessary to include --known-splicesite-infile option in following HISAT2 mapping? I worry this option slow mapping without increase mapping performance much. Thank you very much for your suggestions.

Answer 1

[GenoMax]

See: HISAT2 command help

[biolab]

Thanks a lot! genomax