From e7175205519ce83e9fa1fedbd72543e7d53c74e9 Mon Sep 17 00:00:00 2001 From: "Yun (Leo) Zhang" Date: Fri, 7 Oct 2022 09:53:02 -0500 Subject: [PATCH] update hisat-3n docs --- docs/_pages/hisat-3n.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/_pages/hisat-3n.md b/docs/_pages/hisat-3n.md index 692bdf14..1ada69d8 100644 --- a/docs/_pages/hisat-3n.md +++ b/docs/_pages/hisat-3n.md @@ -123,7 +123,13 @@ HISAT-3N uses the HISAT2 argument but has some extra arguments. Please check [HI For example, you build your index with basename 'genome' by HISAT-3N-build, please enter `-x genome`. * `--directional-mapping` - Make directional mapping. Please use this option only if your sequencing reads are generated from a strand-specific library. + Make directional mapping. Please use this option only if your sequencing reads are generated from a strand-specific library. + This is for the reads that read1 maps to the forward-strand of reference and the read2 maps to the reverse-strand of reference. + The directional mapping mode is about 2x faster than the default (non-directional) mapping mode. + +* `--directional-mapping-reverse` + Make reverse directional mapping. Please use this option only if your sequencing reads are generated from a strand-specific library. + This is for the reads that read1 maps to the reverse-strand of reference and the read2 maps to the forward-strand of reference. The directional mapping mode is about 2x faster than the default (non-directional) mapping mode. * `--repeat-limit `