Map Ionproton reads

[DNAjunk]

Hi all

How to best align Ionproton RNASeq reads with gaps (spliced) to a reference genome?

TMAP does align those reads but not gapped, right?

I tried GSNAP and GMAP but they both crash at some point (maybe due to the many indels in the Iontproton reads).

Thanks!

[Michael.Ante]

I tried the STAR aligner, as well as BBMAP.
Both worked fine and fast.