From dd90d9dde61b4d70ba6948adc4a81167f629d354 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 4 Apr 2025 16:34:40 -0400 Subject: [PATCH] caution that the splice:sr is experimental --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4d39499..0d7475d 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ cd minimap2 && make ./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 (RNA-seq) ./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions -./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236 or later) +./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236+; experimental) ./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 @@ -40,7 +40,7 @@ man ./minimap2.1 - [Map long mRNA/cDNA reads](#map-long-splice) - [Find overlaps between long reads](#long-overlap) - [Map short genomic reads](#short-genomic) - - [Map short RNA-seq reads](#short-rna-seq) + - [Map short RNA-seq reads (experimental & evolving)](#short-rna-seq) - [Full genome/assembly alignment](#full-genome) - [Advanced features](#advanced) - [Working with >65535 CIGAR operations](#long-cigar) @@ -231,14 +231,16 @@ 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. -#### Map short RNA-seq reads +#### Map short RNA-seq reads (experimental & evolving) ```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. +similarly to `sr` except that it performs spliced alignment. Note that this +functionality is ***experiemental*** and evolving. It is better not to use it +for production. #### Full genome/assembly alignment