Hi Jeremy, Thanks for your help. I'm mapping reads from one organism to a related but different organism, so some of the parameters I'd like to adjust are to relax mapping stringency -specifically:
-n 3 (allow 3 mismatches in seed) -e 250 (allow cummulative phred score of 250 [or some other value depending on read length] for mismatches in remainder of read) I'd also like to only report alignments that are unambiguously mapped to a single location, so: -m 1 --best on --strata on It sounds like I need to read the documentation again, but it didn't look at first glance like I could specify these things. Jeremy On Wed, Nov 16, 2011 at 12:18 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote: > Jeremy, > > My apologies if this has been covered before but I am using Galaxy Main > and wonder if, when running TopHat, you can modify the mapping parameters > used by Bowtie? > > > Not all Bowtie parameters can be modified when running Tophat. Which > parameters are you looking to modify and why? > > It seems that the full parameter list for TopHat pertains only to the > reads that aren't mapped by Bowtie (the reads spanning splice junctions). > > > This should not be the case. For instance, documentation for the > max-multihits discusses multiple hits when mapping reads junctions/segments: > > http://tophat.cbcb.umd.edu/manual.html > > If you're seeing different results, it may be a bug that could be > discussed with the Tophat authors: tophat.cuffli...@gmail.com > > Is there a way to access the full parameter list of Bowtie through TopHat? > > > Not currently. > > Or perhaps run Bowtie directly, then feed this into a TopHat run? > > > I don't think this is possible b/c Tophat uses the reads that map > initially to build the coverage islands and then uses these islands to > generate an index of potential splice junctions. > > Best, > J. > > > > >
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