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Old 07-03-2015, 02:56 AM   #2
annaprotasio
Junior Member
 
Location: UK

Join Date: Feb 2008
Posts: 6
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hi Dan,

Have a look at "samtools flagstat"

The output will looks something like this and I think it contains all the info you requested.

Code:
7276199 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
7276199 + 0 mapped (100.00%:-nan%)
7276199 + 0 paired in sequencing
3787000 + 0 read1
3489199 + 0 read2
6195536 + 0 properly paired (85.15%:-nan%)
6795026 + 0 with itself and mate mapped
481173 + 0 singletons (6.61%:-nan%)
480036 + 0 with mate mapped to a different chr
480036 + 0 with mate mapped to a different chr (mapQ>=5)
good luck
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