--initial-read-mismatches and --segment-mismatches are the two values passed to "bowtie -n" or "bowtie -v" at different Bowtie searches in the TopHat pipeline. I'm not sure you can control the -l or -e Bowtie values from the TopHat command line and so you'll probably have to edit the tophat python code to do it.
Chris
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TopHat BowTie -n mode
Someone must have already asked this question before but I couldn't find any straight answer so posting it again (sorry for the redundancy).
If I want to run TopHat on longer reads (say >75 bps from Illumina) I'll definitely need to allow more mismatches in the alignment. I can adjust it using "--initial-read-mismatches" and "--segment-mismatches" option.
Is there any upper limit on the number of mismatches that TopHat can accept?
If I want TopHat to run BowTie in -n mode, how do I change seed mismatches (-n), seed length (-l) and -e values?
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