How does csaw handle multiply aligned reads?
I guess csaw would not want to use such reads, but I could not find anything in the users guide or manual about what csaw does with multimapped reads.
Does it read a flag in the bam file telling it the alignment is multimapped and then discards it? If the onus is on the user to remove such reads, it would be nice if the manual could be updated with a heads-up.
Thanks for csaw, btw.