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Old 10-27-2015, 10:56 PM   #6
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Location: Montreal

Join Date: May 2013
Posts: 367

I don't have this problem when I use BWA mapping. But it's better to use Bowtie for E. coli reads since BWA looks for intron so better used for eukaryotes is that right ?
No, BWA, like Bowtie does not take into account the introns.
Only splice-junction aware aligners, like TopHat and STAR do, in which case you have to provide them with the genome annotation indicating the location of the junctions.
TopHat actually delegates the alignment to Bowtie1 or 2, and only handles the splicing.

In the link to the Galaxy instance that you posted, you are using a version of Bowtie that dates back to 2010, version 0.12.7. It's not clear from your post if you've already tried this, but the first troubleshooting step I would take would be to upgrade to a more modern version of Bowtie. There is a long list of bugs that have been fixed in Bowtie since 2010.
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