Bowtie mapping with distance to next best hit

[droog_22]

Hi,

I am using bowtie 0.12.7 to map 50mer paired-end Illumina reads to the hg19 assembly. With this command:

bowtie -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa

I am getting the best and uniquely mapped positions. I am wondering if there was an option or a workaround to map the reads in a way that I only print out a mapped position if the next mapped read-pair has at least 2 more mis-matches to the reference genome. So say my hit has 0 MM to hg19, the next best hit has a total of 4MM, then print the 0 MM hit. Do not print the 0 MM hit if the next best hit has e.g. 1MM to the reference.

Thanks, Daniel

[amitm]

I guess if you sort the SAM file (then reads would be ordered wrt genome mapping) then you can write a script to parse the CIGAR field (column 6) and do the desired.