View Single Post
Old 09-19-2013, 11:30 PM   #3
kokonech
Curious Character
 
Location: Berlin, Germany

Join Date: Sep 2010
Posts: 13
Default

Hi!

Make sure the BAM file is sorted by coordinate and the splitted alignment is defined by N cigar code (true for tophat by default).

Also you might check some alternative ways to calculate coverage, for example using coverageBed and intersection with annotation file:
http://okko73313.blogspot.de/2013/04...hromosome.html
kokonech is offline   Reply With Quote