Question: Is it necessary to include --known-splicesite-infile in HISAT2?
0
gravatar for biolab
3.3 years ago by
biolab1.2k
biolab1.2k wrote:

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.

hisat2 • 1.9k views
ADD COMMENTlink written 3.3 years ago by biolab1.2k
1

See: C: HISAT2 command help

ADD REPLYlink written 3.3 years ago by genomax91k

Thanks a lot! genomax

ADD REPLYlink written 3.3 years ago by biolab1.2k
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