> 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.cuffli...@gmail.com Good luck, J. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/