modifying bowtie settings from tophat

[hmortens]

*Hi,
I am attempting to modify the default settings that Tophat specifies for Bowtie to improve alignments.
I have tried the -g, -k, and -m options from within tophat. I am not getting tophat to recognize the -k option. just get the tophat: option -k not recognized are you able to get this to work?
It seems like the appropriate options in bowtie would be -n, -a, --best, and --strata. But tophat does not recognize.
The most critical I think would just being able to view the number of valid alignments in order (best->worst).any suggestions would be appreciated.
Is it necessary to modify the python code to make this happen (hopefully not!)?
thanks.
holly

[mgogol]

"Is it necessary to modify the python code to make this happen?"

Yes. If you want to modify bowtie parameters that are not available in tophat, the only way would be to modify the tophat python script.

You could use bowtie instead of tophat, depending on what you are doing -- you could align to the transcriptome instead of the genome, for example, if you're worried about losing splice junction reads...