I understand that, when a single read is mapped in multiple parts, it can be considered as a single cDNA (depending on the gap's length between the 2 fragments). but how do you do peak calling for multi-mapped reads? are they ignored? especially for the permutation test.
Hi,
I have a question regarding multi-mapped reads.
I understand that, when a single read is mapped in multiple parts, it can be considered as a single cDNA (depending on the gap's length between the 2 fragments). but how do you do peak calling for multi-mapped reads? are they ignored? especially for the permutation test.
Thank you !