From 248158a3e1349e45f902ec6247cf4b8c7f9a3bba Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 30 May 2018 11:03:16 -0400 Subject: [PATCH] Resolved #168: citing the manpage for cs --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index dae44fe..00a9740 100644 --- a/README.md +++ b/README.md @@ -253,7 +253,9 @@ similar to the `MD` SAM tag but is standalone and easier to parse. If `--cs=long` is used, the `cs` string also contains identical sequences in the alignment. The above example will become `=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both -reference and query sequences in one string. +reference and query sequences in one string. The `cs` tag also encodes intron +positions and splicing signals (see the [minimap2 manpage][manpage-cs] for +details). #### Working with the PAF format @@ -365,3 +367,4 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`. [issue]: https://github.com/lh3/minimap2/issues [k8]: https://github.com/attractivechaos/k8 [manpage]: https://lh3.github.io/minimap2/minimap2.html +[manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10