Hey, I am a newbie in pysam, and now I have a question.
I use pysam to find the reads which overlap a given position, and then I want to get the nucleotides at this position in each read. Followed my code:
position is an given location(0 based)
reads = [read for read in samfile.fetch(chr_name, position,position+1)] for read in reads: neu1 = read.seq[read.get_reference_positions().index(position)] neu2 = read.seq[position-read.reference_start] neu3 = read.query[position-read.reference_start-read.qstart]
I want to know which is right, neu1, nue2, nue3, or others? thk!