hello every one,
after running bowtie2 by using "bowtie2-align -f AT_ref -f GAC.fasta -S 1.sam" and got the details summery 616571 reads; of these:
616571 (100.00%) were unpaired; of these:
180433 (29.26%) aligned 0 times 306495 (49.71%) aligned exactly 1 time 129643 (21.03%) aligned >1 times,
as I guess, my chimeric reads would be in 129643 (21.03%) aligned >1 times out of 616571 reads; but I am not be able to extract these alignments from my output sam file. I don't know how to write syntax for this purpose. please suggest me.