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 genome) to assemble gtf
> transcript files produced by Cufflinks for each group of 3 Illumina
> paired-end reads corresponding to biological replicates, in order to use the
> resulting combined gtf file for comparing the TopHat alignments of two such
> groups using cuffdiff.
>
> Is there any difference in the output between cuffdiff and cuffcompare, using
> in this fashion? For example, do they form the "union" of transcripts by the
> same rules, and do their outputs contain (or lack) the same columns (strand,
> perhaps??) I've read things on seq-answers indicating that I should be using
> cuffmerge, but I can't find it on the public server and apparently haven't
> installed it properly on my own computer so far.
From the Cufflinks/compare/merge/diff documentation (
http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge ):
*Cuffmerge calls Cuffcompare and does some filtering of transfrags as well as
merging of novel and known isoforms;
*"The main purpose of this script is to make it easier to make an assembly GTF
file suitable for use with Cuffdiff."
Hence, it appears that Cuffmerge and Cuffcompare are relatively similar and use
the same basic union algorithm--whatever Cuffcompare uses. If you have more
detailed questioned, you might ask the Cufflinks' authors:
tophat.cuffli...@gmail.com
Good luck,
J.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
