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Old 09-20-2016, 12:19 AM   #2
Senior Member
Location: Vienna

Join Date: Oct 2011
Posts: 123

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. from the RSeQC tools.
Furthermore, I'd check the read files with FastQC before and after trimming.

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.

Michael.Ante is offline   Reply With Quote