View Single Post
Old 10-28-2014, 03:21 PM   #11
I like code
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

To cut down on the possible complexity of what is going wrong, try aligning only one of the two mate files with Tophat (i.e. as a single-end alignment) and see if Tophat manages to align more data. long are your reads and what are you aligning to?
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll is offline   Reply With Quote