Hi, I recently performed an RNA immunoprecipitation followed by SOLiD sequencing (50 bp fragmented reads). I haven't received my first SOLiD sequencing results yet, but I was told I should have them soon. I've tried doing my own research on how to map, align, and plot my results but I don't have a concrete workflow as to how I will analyze my results yet. I have very little experience doing any programming and would prefer to use galaxy. There are labs on my campus I can go to to get my color space data mapped, but I would like to do things myself. Is there a way on galaxy (or another program) to convert my color space data to sequence, then map those reads to the yeast transcriptome and analyze it? Even if you can't answer my question directly I'd appreciate any tips from anyone who has worked with RNA-seq data already.
Thanks in advance