On Wednesday, August 7, 2013, Nikhil Mallela wrote:

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.

What is bad is converting FASTA without qualities to FASTQ with made up qualities, regardless of if this is sequence or color space.

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

Do you have the quality scores for your data, in a *.qual file normally.

Peter