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.


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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