[galaxy-user] cuffmerge question

I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find an answer in the Galaxy-user or Seq-answers archives. My question is, if I use the public Galaxy server interface to TopHat and Cufflinks, is there any access to cuffmerge? Also, I'm trying to

Re: [galaxy-user] Any thing wrong with my cufflink process in galaxy?

Yao, It's difficult to tell what's wrong without seeing your analysis. However, you may want to use the reference annotation during the Cufflinks phase to either estimate isoform expression or guide assembly (this option will appear on our public server soon). Read the Cufflinks documentation

Re: [galaxy-user] cuffmerge question

Carol, My question is, if I use the public Galaxy server interface to TopHat and Cufflinks, is there any access to cuffmerge? No, Cuffmerge is not available in Galaxy. Also, I'm trying to understand the difference between using cuffmerge and then using cuffcompare (without a reference

[galaxy-user] (no subject)

Hi Jeremy, I tried to run cufflinks to assemble transcripts after running Tophat against my own reference. This error was encountered. What was wrong? How to fix it? Error running cufflinks. [21:01:14] Inspecting reads and determining fragment length distribution. Processed 11130 loci.