View Single Post
Old 06-23-2011, 04:38 PM   #6
Jon_Keats
Senior Member
 
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279
Default

Maybe try BWA in single end mode, filter out the reads aligning to multiple locations, then manually pair the reads using perl or something to find the mates/pairs that mark the ends of your RNA species
Jon_Keats is offline   Reply With Quote