I want to identify the actual pairs of reads in a SAM file that potentially has multiple alignments for the same given pair.
Is it sufficient to check whether two lines in the SAM file have same QNAME?
Do I have to check for POS (start) and PNEXT (start of mate) fields and make sure they are matching between two lines?
I am aware of the meaning of SAM flags to identify paired and mapped reads. Simply checking the flag, however, does not allow me to identify the actual pair.
Thanks in advance.
Is it sufficient to check whether two lines in the SAM file have same QNAME?
Do I have to check for POS (start) and PNEXT (start of mate) fields and make sure they are matching between two lines?
I am aware of the meaning of SAM flags to identify paired and mapped reads. Simply checking the flag, however, does not allow me to identify the actual pair.
Thanks in advance.
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