View Single Post
Old 09-20-2016, 12:19 AM   #2
Michael.Ante
Senior Member
 
Location: Vienna

Join Date: Oct 2011
Posts: 123
Default

Hi Rangika,

2nd first:
You need to be aware of the fact that samtools flagstat produces statistics on alignments. Meaning, a read can align multiple time and will occur multiple times in the flagstat output. You may check your alignment file with e.g. bam_stat.py from the RSeQC tools.
Furthermore, I'd check the read files with FastQC before and after trimming.

So:
1) I'd check a set of different data sets to choose which way to go. Also, I would not rely on the %mapped from samtools flagstat.

Cheers,
Michael
Michael.Ante is offline   Reply With Quote