I am trying to extract all the reads which : 1) mapped to 5' -> 3' OR 3' -> 5' of reference sequence AND 2) paired but one of the reads is unmapped.
However, to meet requirement 1), out of the flags stated above, what is the simple method to determine whether the reads are mapped to 5' -> 3' OR 3' -> 5' of the reference sequence?
I have also read from slide 32 of here but was quite difficult when I start to consider combinations.
Thanks a lot!!!