I have used bowtie2 --local for mapping my sequence data against a reference genome. I have filtered the multi-mapped reads from the .bam file and would like to find the different locations on the genome for each of these multi-mapped reads. Here while mapping, I have not used the -k attribute.
Hi,
I have used bowtie2 --local for mapping my sequence data against a reference genome. I have filtered the multi-mapped reads from the .bam file and would like to find the different locations on the genome for each of these multi-mapped reads. Here while mapping, I have not used the -k attribute.
Any suggestions, please?
Thank you!