Entering edit mode
7.4 years ago
jt358
▴
10
Hi all,
I have a round 350 sample files currently in SAM format, but can convert to bam in samtools. What I want to do is produce a excel file or such like, which contains all the information from the flagstat command regarding number of reads that have mapped etc. I can print individual data as each sample is processed singularly but obviously a cut and paste job of 450 samples will take forever (and I'm sure is unnecessary) Could someone offer any advice kindly?
Many thanks
Jamie
Take a look at MultiQC.