From ff312a29571b3a90b27ebf705f3daf6f03c02fd3 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 13 Apr 2025 17:14:44 -0400 Subject: [PATCH] documented 2-pass in README --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 600ae8c..2017b07 100644 --- a/README.md +++ b/README.md @@ -241,6 +241,9 @@ mixed. minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation +# 2-pass alignment +minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed +minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam ``` The new preset `splice:sr` was added between v2.28 and v2.29. It functions similarly to `sr` except that it performs spliced alignment. Note that this