Hi,
I am using bowtie 0.12.7 to map 50mer paired-end Illumina reads to the hg19 assembly. With this command:
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
I am using bowtie 0.12.7 to map 50mer paired-end Illumina reads to the hg19 assembly. With this command:
Code:
bowtie -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa
Thanks, Daniel
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