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. Cheers, Enis On Sun, Jan 13, 2013 at 9:58 PM, Nuphar Salts <nupharsalts@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.