[galaxy-dev] Can I analyze *.csfasta & *.xsq data on Galaxy ?

Hi,

I am working on the colorspace data. I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl). I wanted to use tophat and cufflinks pipelines with Galaxy, Although tophat can make use of colorspace data, but galaxy seems to be accepting only FASTQ format for most of its tools. And the online community is strongly discouraging the conversion of colorspace to FASTQ.

So, is there any work-around for this problem ? Do I have to modify the scripts according to my requirement in my local installation ?

Looking forward for your advise.

Thanks in advance, Nikhil.