Question: Solid Rna-Seq De Novo Transcriptome Assembly
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Oscar,
You most likely want to explore tools that are designed specifically
for
this purpose, if the reference genome you are talking about is the
assembled transcriptome. Trinity is one tool, but there are others in
the Tool Shed and on some of the Public Servers.
Links:
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server
http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://wiki.galaxyproject.org/BigPicture/Choices
http://wiki.galaxyproject.org/Tool%20Shed
Your question is a bit confusing because the 'annotations' may already
be what these tools would produce and I am not sure what you are
trying
to do next. If it is the assignment of putative function, then there
are
many paths to follow, some better suited for viral genomes. You'll
want
to find out what others doing this exact work are using right now and
consider the same tools. Start by checking out the public Galaxy
servers, many have trial tools that you can later include in a
local/cloud from the tool shed:
http://wiki.galaxyproject.org/PublicGalaxyServers
If your question was misunderstood (the reference genome is in fact a
DNA genome - and you have RNA sequence to align), then the RNA-seq
pipeline can be used as-is with 'Tophat for SOLiD', Cufflinks,
CuffMerge, CuffDiff - all on a local/cloud/slipstream with the
reference
genome as a cluster reference genome. There is no requirement for
reference annotation with any of these tool - it helps to gain full
functionality - especially with CuffDiff, but is not required. More
assistance is at tophat.cufflinks@gmail.com.
Hopefully this helps,
Jen
Galaxy team
--
Jennifer Hillman-Jackson
http://galaxyproject.org