This may be a question already and repeatedly asked before, but I could not find an answer relevant to my issue...
I would like to map human/mouse genome sequence data of paired end reads (150 bp x 2 etc.) allowing one end being "uniquely" mapped and the other end "multiply" mapped in order to increase mappability to repetitive regions.
Is this (one end uniquely and the other end multiply mapped) possible for common mapping softwares such as bowtie2, bwa etc. by properly setting some option parameters, or do I need to manually filter (by awk etc.) the output, for which I allow for multimapping reads of both ends?
Thank you for your kind help and advice in advance. schu is offline Reply With Quote