fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-04 05:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

document --spsc

Browse Source
This commit is contained in:
Heng Li
2024-10-12 23:27:46 -04:00
parent 68179ed195
commit 3e1ab2951d
3 changed files with 21 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
minimap2.1
+19 -3
View File
@@ -433,6 +433,21 @@ on SIRV data, please add
.B --splice-flank=no
to the command line.
.TP
.BR --spsc \ FILE
Splice scores []. Each line consists of five fields: 1) contig, 2) offset, 3) `+' or `-', 4) `D' or `A', and 5) score,
where offset is the number of bases before a splice junction, `D' indicates the
line corresponds to a donor site and `A' for an acceptor site.
A positive score suggests the junction is preferred and a negative score
suggests the junction is not preferred.
.TP
.BR --junc-pen \ INT
Penalty for a position not in FILE specified by
.B --spsc
[5]. Effective with
.B --spsc
but not
.BR --junc-bed .
.TP
.BR --junc-bed \ FILE
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.
@@ -440,9 +455,10 @@ 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
.BR --junc-bed )
[9].
Score bonus for a splice donor or acceptor found in annotation [9]. Effective with
.B --junc-bed
but not
.BR --spsc .
.TP
.BI --end-seed-pen \ INT
Drop a terminal anchor if