bowtie used by tophat

[liuxq]

I find that tophat uses bowtie with parameter "-v 2", which will discard many low quality reads dramatically.

Is there a method to control the bowtie parameters used by tophat?

Why tophat does not use default -n mode for bowtie reads mapping?

[Daehwan]

I find that tophat uses bowtie with parameter "-v 2", which will discard many low quality reads dramatically.

Is there a method to control the bowtie parameters used by tophat?

Why tophat does not use default -n mode for bowtie reads mapping?

I think this is a very good point, I'll make a new option for users to choose between "n" and "v" option in the next release!!

Thanks,
Daehwan

[peromhc]

Many of us have hoped to be able to customize how Bowtie is implemented within Tophat for a long time now.. Is there any reason for this limitation, other that time spent coding the different options into Tophat?

[xinwu]

I have another feature request about bowtie trimming option both from 3 end and 5 end. So far, we have to trim the low quality bases manually and it take redundant space for trimmed read files.