From 43ce69104d4b31e38135307fac8b1f9e5fc9363a Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 15 Sep 2014 23:59:35 -0400 Subject: [PATCH] Removed PacBio read-to-read instruction --- README.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/README.md b/README.md index be4bc99..58322d4 100644 --- a/README.md +++ b/README.md @@ -87,16 +87,12 @@ settings: * Illumina paired-end reads no longer than ~70bp: bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai - bwa samse ref.fa reads.sai reads.fq > aln-pe.sam + bwa samsp ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam * PacBio subreads to a reference genome: bwa mem -x pacbio ref.fa reads.fq > aln.sam -* PacBio subreads to themselves (the output is not SAM): - - bwa mem -x pbread reads.fq reads.fq > overlap.pas - BWA-MEM is recommended for query sequences longer than ~70bp for a variety of error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small.