Samtools

bwa-mem multi-mapping reads

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…

Downsampling bam files to a certain number of reads

When compare different ChIP-seq data sets or analyze a set of ChIP-seq data sets together (e.g. ChromHMM analysis), it is desirable to subsample the deeply…

rehead a bam file

I downloaded some ChIP-seq bam files from the UCSC genome browser

count how many mapped reads in a bam file

I wanted to count how many mapped reads are in a ChIP-seq bam file downloaded from UCSC ECODE project.