After reading the SAM specs it is still not very clear what is the meaning of these two fields in the FLAG:
- SEQ being reverse complemented
- SEQ of the next segment in the template being reversed
Could you please explain it to me?
UPDATE: if I understood it well when "SEQ being reverse complemented" is NOT SET it means that the read has been aligned to the forward strand, when SET it means that it has been aligned on the reverse strand. Is that correct?
And can we use these fields to detect an incorrect orientation of a paired-end read ?