Re: [galaxy-user] Changing Bowtie parameters in TopHat

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

Re: [galaxy-user] Changing Bowtie parameters in TopHat

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

Re: [galaxy-user] Changing Bowtie parameters in TopHat

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