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r934: --junc-bed to read BED12

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Heng Li
2019-04-28 20:12:28 -04:00
parent f64e426a5a
commit 49c6d83a8e
4 changed files with 45 additions and 19 deletions
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@@ -1,4 +1,4 @@
.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r933)" "Bioinformatics tools"
.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r934)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -365,10 +365,10 @@ on SIRV data, please add
to the command line.
.TP
.BR --junc-bed \ FILE
BED file consisting of annotated introns and their strands. With this option,
minimap2 prefers splicing in annotations.
.I FILE
can be generated with `paftools.js gff2bed -j ann.gtf' [].
Gene annotations in the BED12 format (aka 12-column BED), or intron positions
in 5-column BED. With this option, minimap2 prefers splicing in annotations.
BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'
[].
.TP
.BR --junc-bonus \ INT
Score bonus for a splice donor or acceptor found in annotation (effective with