With and without mismatches I find that some (up to 1/3) of my paired end reads only have one of the two mates align.
So, how does tophat deal with paired ends?
How might this affect downstream analysis (like cufflinks)?
How have other people dealt with this?
thanks!
So, how does tophat deal with paired ends?
How might this affect downstream analysis (like cufflinks)?
How have other people dealt with this?
thanks!