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.goecks@emory.eduwrote:

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.cufflinks@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.