Bowtie: Paired End Alignment With Norc/Nofw
Is --norc/--nofw (no alignment with reverse complement/forward reference sequence) compatible with paired end alignment?
If I am going for the default --fr (forward-reverse) mate alignment, then:
are the mate-2 sequences reverse complemented and aligned or they are aligned to RC -reference. If latter is the case then --norc/--nofw might be incompatible; how to force mate-1 alignment to only forward reference sequence ?
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Bharat Iyengar
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okay.. i found out that
--norc/--nofwwont work with paired end reads with--fr/-rfspecified. So it means that the mate-2 is aligned to the RC-reference.I shall delete the question if it is of not much use.