[bigfoot]

Dear Nate,

I am actually considering doing some RNAseq analysis on non-model organism (with reference transcriptome, but no genome) using SOLID data. Did you finally succeed in mapping your SOLID data to your reference transcriptome?

Cheers,

Marie

[JueFish]

Marie,

Sorry for the long delay, but I lost track of this thread. Yes, I did finish a bunch of this work, so if you still have any specific questions about what we did, please either add to this thread or drop me a line. Basically, we used SOLiD data in both de novo assembly and subsequent RNA-seq and other analyses.

Cheers,
Nate

[tonup69]

I am trying to do RNAseq on SOLiD data now and would like to do the work in GALAXY. I did notice the poor quality scores for the .csfastq and the .qual files generated from the xsq files. In fact, when I filtered reads below a quality score of 20 I only got back .67% of the data! Should I go ahead with the untrimmed csfastq files or should I change trim parameters?

[twaddlac]

I would try them both. Every data set is different so I'm not sure how either will change the data but it won't hurt to try. In my experience, the filtered SOLiD data yielded better results.