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.