[galaxy-user] Map with Bowtie or Tophat?

Hi all, what is the difference between using "NGS:mapping---Map with Bowtie for Illumina" and "NGS: RNA analysis-Tophat for Illumina" when mapping reads against a reference/custom genome? thanks, ib ___ The Galaxy User list should

[galaxy-user] cuffdiff with three groups

Dear all, I ran Cuffdiff with 3 groups: A, B, C each with 2, 5 and 1 replicates respectively. When looking at the transcripts dif.exp.testing, I have only sample A and B and redpective values. What happened to sample C? Thanks for any help. ib _

Re: [galaxy-user] cuffdiff with three groups

Sorry, I did not read carefully. All three samples are listed, just down in the column I found the other sample. ib On Sat, Aug 11, 2012 at 7:41 PM, i b wrote: > Dear all, > I ran Cuffdiff with 3 groups: A, B, C each with 2, 5 and 1 replicates > respectively. > When looking at the transcripts d

[galaxy-user] Extreme parallelization for NGS analysis

I'd like to start an open discussion on the topic of parallelization for NGS data. I noticed that Galaxy recently came out with a cloud-based interface using Amazon EC3. I've been trying to learn more about how these NGS analysis algorithms (for alignment, assemly, etc.) are actually implemented in