Tailseeker 3 uses STAR as the primary sequence alignment software. Optionally, GSNAP can be used to rescue unmapped sequences by STAR. Tags with long poly(A) tails sometimes suffer from low sequence read quality, and this leads to failure in identification of tags. Usually, GSNAP rescues ~0.5% of total reads and ~10% among long poly(A) tails. However, it lengthens total running time of the pipeline by about 10-fold.
Do you want to use GSNAP together with STAR?
Please copy the following configuration and save it as a file named “tailseeker.yaml” in an empty directory. And, run “tseek run -j” there.