From 8e606bcc06c9411b74bb8919826209a06607b802 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 6 Aug 2018 09:08:33 -0400 Subject: [PATCH] added a `-C5` example to Getting Started --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7512210..1f6bc95 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,9 @@ cd minimap2 && make ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./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 -./minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq +./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 -uf -C5 ref.fa query.fa > aln.sam # Final PacBio Iso-seq or traditional cDNA ./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