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Old 03-26-2015, 05:30 AM   #1
DNAjunk
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Location: Western Europe

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Default Map Ionproton reads

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!
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Old 03-26-2015, 06:33 AM   #2
Michael.Ante
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I tried the STAR aligner, as well as BBMAP.
Both worked fine and fast.
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