I would like to count the number of tags that are mapped across splice junctions from Tophat output. I just counted the number of reads (Col 5) from junctions.bed that are generated from tophat out. The % of reads across junctions is around 30% which is way high. Am I missing anything??
Basically I want to count the number of reads mapped across splice junctions. Thanks.
Basically I want to count the number of reads mapped across splice junctions. Thanks.