Changing Bowtie parameters in TopHat
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? 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). Is there a way to access the full parameter list of Bowtie through TopHat? Or perhaps run Bowtie directly, then feed this into a TopHat run? Thanks, Jeremy
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.
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.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.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.
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.
Yes, reading the documentation is highly recommended. You can definitely specify -m, but you may have to think creatively about how to modify Tophat's available parameters to meet your needs. You might also contact the Tophat authors directly and see if they have any suggestions: tophat.cufflinks@gmail.com Good luck, J.
participants (2)
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Jeremy Coate -
Jeremy Goecks