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

Join Date: Jun 2009
Posts: 61
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).

DNAjunk is offline   Reply With Quote
Old 03-26-2015, 06:33 AM   #2
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Location: Vienna

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I tried the STAR aligner, as well as BBMAP.
Both worked fine and fast.
Michael.Ante is offline   Reply With Quote

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