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update hisat-3n docs #389

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update hisat-3n docs #389

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8 changes: 7 additions & 1 deletion docs/_pages/hisat-3n.md
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Expand Up @@ -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 <int>`
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