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.

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