Hi,
Can someone tell me what flag I should grep for in order to
obtain reads that are outward facing (mate pairs: <--- && ---> ) and what
flags I should grep for in order to obtain reads that are inward facing (paired ends: --> && <---)?
many thanks
Les
p.s. I have consulted the picard's useful site at http://picard.sourceforge.net/explain-flags.html
but what confuses is me that the definition of "proper pair" etc which is dependent on the aligner's definition based on the insert size.
Can someone tell me what flag I should grep for in order to
obtain reads that are outward facing (mate pairs: <--- && ---> ) and what
flags I should grep for in order to obtain reads that are inward facing (paired ends: --> && <---)?
many thanks
Les
p.s. I have consulted the picard's useful site at http://picard.sourceforge.net/explain-flags.html
but what confuses is me that the definition of "proper pair" etc which is dependent on the aligner's definition based on the insert size.
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