Hi Nuphar,
I believe yu should be using a tool that is color-space aware and not
converting the data - Galaxy Main has 'Bowtie for SOLID' available, which
should understand your data as is.

BTW, for these types of questions, you should send the email to galaxy-user
mailing list (http://lists.bx.psu.edu/listinfo/galaxy-user), which I have
CC'd now, because that will get your question much more exposure and thus
higher likelihood of a useful answer.


On Sun, Jan 13, 2013 at 9:58 PM, Nuphar Salts <nupharsa...@gmail.com> wrote:

> Hello,
> We're trying to convert csfasta and qual files to fatsq, using galaxy.
> The problem is that it seems that A is always used as the first base, for
> each number representing a color.
> We want to use bowtie for analyzing RNA-seq results.
> Is it possible to convert our files with galaxy or should we use another
> tool?
> Thanks,
> Nuphar.
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