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?