hello. first, sorry for that I'm not good at this field. I aligned reads to reference, and now I'm finding each read's start location from start codon to draw ribosome footprint figure. My question is
how to treat FLAG 16. I understand that they aligned to reverse strand, so they expressed in reverse complement forms in sam files. so if i have
FLAG:16, is it correct to point
read1in 25 location from start codon in ribosome footpring? Just treat like other flag0 reads?
why we have reverse strand sequence in reads?