From fc2d1e95b34873241304accf966fed694947c043 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 2 Apr 2025 11:24:44 -0400 Subject: [PATCH] document splice:sr in README --- README.md | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c94ba85..34c674f 100644 --- a/README.md +++ b/README.md @@ -18,9 +18,10 @@ cd minimap2 && make ./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27 or later) ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) -./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore Direct RNA-seq -./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # Final PacBio Iso-seq or traditional cDNA +./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq +./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq or traditional cDNA ./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # prioritize on annotated junctions +./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236 or later) ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap @@ -39,6 +40,7 @@ man ./minimap2.1 - [Map long mRNA/cDNA reads](#map-long-splice) - [Find overlaps between long reads](#long-overlap) - [Map short accurate genomic reads](#short-genomic) + - [Map short RNA-seq reads](#short-rna-seq) - [Full genome/assembly alignment](#full-genome) - [Advanced features](#advanced) - [Working with >65535 CIGAR operations](#long-cigar) @@ -216,7 +218,7 @@ the overlapping mode because it is slow and may produce false positive overlaps. However, if performance is not a concern, you may try to add `-a` or `-c` anyway. -#### Map short accurate genomic reads +#### Map short genomic reads ```sh minimap2 -ax sr ref.fa reads-se.fq > aln.sam # single-end alignment @@ -229,8 +231,14 @@ be paired if they are adjacent in the input stream and have the same name (with the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be mixed. -Minimap2 does not work well with short spliced reads. There are many capable -RNA-seq mappers for short reads. +#### Map short RNA-seq reads + +```sh +minimap2 -ax splice:sr ref.fa reads-se.fq > aln.sam # single-end +minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # paired-end +``` +The new preset `splice:sr` was added between v2.28 and v2.29. It functions +similarly to `sr` except that it performs spliced alignment. #### Full genome/assembly alignment