1) Redo the mapping with bowtie or bwa, what is the option to accomplish this? -k 0 does not work!
2) Filter out the SAM/BAM file. What is the option to filter no-mismatch!
Seems not enough information about the option "H:i:0"
I search over this forum and biostar, many discussion with the unique mapped reads, ot unmapped reads. No discussion about the perfectly mapped reads, i.e. mapped reads without any mismatch.
For column 6 of CIGAR string, I used
Code:
grep "\s\d+M\s"
Can anybody give some suggestion.
Thanks a lot!
Leave a comment: