Question: Changing Bowtie Parameters In Tophat
gravatar for Jeremy Coate
7.0 years ago by
Jeremy Coate70
Jeremy Coate70 wrote:
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
alignment bowtie • 1.4k views
ADD COMMENTlink modified 7.0 years ago by Jeremy Goecks2.2k • written 7.0 years ago by Jeremy Coate70
gravatar for Jeremy Goecks
7.0 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Jeremy, Not all Bowtie parameters can be modified when running Tophat. Which parameters are you looking to modify and why? This should not be the case. For instance, documentation for the max- multihits discusses multiple hits when mapping reads junctions/segments: If you're seeing different results, it may be a bug that could be discussed with the Tophat authors: Not currently. 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.
ADD COMMENTlink written 7.0 years ago by Jeremy Goecks2.2k
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
ADD REPLYlink written 7.0 years ago by Jeremy Coate70
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: Good luck, J.
ADD REPLYlink written 7.0 years ago by Jeremy Goecks2.2k
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