Question: Solid Rna-Seq De Novo Transcriptome Assembly
gravatar for Jennifer Hillman Jackson
5.1 years ago by
United States
Jennifer Hillman Jackson25k 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: 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: 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 Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson
rna-seq cuffmerge cufflinks • 948 views
ADD COMMENTlink written 5.1 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour