https://divingintogeneticsandgenomics.com/tags/bwa/ Recent content in Bwa on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 10 Aug 2017 11:27:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ Thu, 10 Aug 2017 11:27:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ An error I was using TEQC to do quality control of my WES bam files aligned by bwa-mem. My data are paired end, so a function reads2pairs is called to make the paired-end reads to be a single fragment. I then get this error: > readpairs <- reads2pairs(reads) Error in reads2pairs(reads) : read pair IDs do not seem to be unique I asked in the bioconductor support site and went to the source code of that function. https://divingintogeneticsandgenomics.com/archive/bwa-aln-or-bwa-mem-for-short-reads-36bp/ Thu, 15 Jun 2017 12:01:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-aln-or-bwa-mem-for-short-reads-36bp/ My ChIP-seq data are 36bp single end reads. I usually use bowtie1 for mapping ChIP-seq reads, but bowtie1 does not handle indels. Since I want to call mutations on the ChIP-seq reads, I have to use another aligner BWA, the most popular mapper written by Heng Li. The github page says if reads < 70bp, bwa aln should be used. Otherwise, bwa mem should be used. bwa mem is a more recent algorithm (should be better? https://divingintogeneticsandgenomics.com/archive/convert-bam-to-fastq-and-remap-it-with-bwa-mem/ Tue, 06 Oct 2015 15:21:00 -0700 https://divingintogeneticsandgenomics.com/archive/convert-bam-to-fastq-and-remap-it-with-bwa-mem/ Why we want to revert bam files back to fastq file? Sometimes, you get a processed bam file from other resources, but you want to map it with another aligner. For example, the old BWA aln does not keep the information for soft-cliped reads which are useful for structural variant detection, the new BWA mem is more suitable for this. So, I want to dump bam to fastq first and then realign it with BWA MEM.