Hello
I have been analysing a SAM file(alinged by Bioscope) with SOLiD transcriptome paired-end sequences, and the FLAGs were kind of confusing.
FLAG(F3, F5) = (99,147) means the paired reads are mapped properly.
FLAG(F3, F5) = (97, 145) means the paired reads are mapped unproperly.
When I filted FLAG(F3,F5)=(97,145), 10% of the paired reads were mapped in the same chromosome with proper insert size(50< < 50000). I wonder, why the reads seemingly properly mapped were flagged as 97 or 145.
Also, I found similar situations with different orientations
FLAG(F3, F5) = (83, 163) : mapped properly
FLAG(F3, F5) = (81, 161) : mapped unproperly
the reads with FLAG (81, 161) included the reads with proper insert size.
What is the meaning of 'properly aligned' for paired reads?
Thank you
I have been analysing a SAM file(alinged by Bioscope) with SOLiD transcriptome paired-end sequences, and the FLAGs were kind of confusing.
FLAG(F3, F5) = (99,147) means the paired reads are mapped properly.
FLAG(F3, F5) = (97, 145) means the paired reads are mapped unproperly.
When I filted FLAG(F3,F5)=(97,145), 10% of the paired reads were mapped in the same chromosome with proper insert size(50< < 50000). I wonder, why the reads seemingly properly mapped were flagged as 97 or 145.
Also, I found similar situations with different orientations
FLAG(F3, F5) = (83, 163) : mapped properly
FLAG(F3, F5) = (81, 161) : mapped unproperly
the reads with FLAG (81, 161) included the reads with proper insert size.
What is the meaning of 'properly aligned' for paired reads?
Thank you
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