I have aligned SOLiD mate-pair reads using bwa-0.5.9. Now, it is my understanding that SOLiD mate-pair reads are oriented in the same direction
R3 ------> F3 ------>
I am using a downstream application that expects the reads to be aligned pointing inwards.
R3 ------> <------ F3
Would simply reverse-complementing the F3 reads achieve this? If I have an aligned bam file, could I simply reverse complement the read and reverse the quality string or would I need to change any flags as well? Any program to handle this already in the public domain?