Is it necessary to include --known-splicesite-infile in HISAT2?
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.
1 answer
See: HISAT2 command help
Log in to answer this question.
More posts like this
-
Tool: vareffect — a Rust-based variant effect predictor that replaces VEP
written by LIA Genomics •
-
What is the differences in index building by hisat with or without exon, splicing variant files?
written by mathavanbioinfo
-
What is the prefered script for HISAT2 genome-guided using draft genome? --dta or --exon ?
written by Farbod
-
Low read mapping efficiency with HISAT2
written by givans •
-
Am I using Tophat2 correctly? Segment-based junction search error keeps coming up.
written by aswartz85 •
-
Coverage-search vs. no coverage-search in running Tophat
written by tunl
-
Error message whengenerating read coverage tables for Ballgown by stringtie
written by hu.guangzhen9 •
-
RNA seq NGS data analysis
written by poonam.bi01 •
-
Output unmapped reads to a file when using tophat2
written by biolab
-
bowtie problem: cannot locate bowtie index
written by biolab
