I have read the Tophat 1.4 manual, however I do not seem to understand the outputs very well.
I used a reference genome for my alignment with Tophat and I got a file called "accepted_hits.bam"
This file's cigar strings don't contain any soft clips (S). Can someone explain me why this is happening ?
Also, this was for the reference genome. If I wanted to align to a junction database, should I just use the junction reference instead of the genome reference ? Or does Tophat align to junctions automatically ?
Very confused with the documentation.