Hello John,
Sorry for the delay in getting back to you.
It is possible to do the type of analysis you are looking to do. I have
just constructed a workflow to take in raw next gen seq data and process
it through tophat, cufflinks, and bowtie. Unfortunately, I can't share
the workflow as it is part of an ongoing project that will be put into a
paper.
You may want to look at using the 'External Tool' to call those
applications from the command line. This should be in the available
services panel. This is how I did it, though I'm not sure if this is
available yet (developers?), in the current Taverna. You basically call
each of those tools using the same commands as you would when running
them from the shell. They can be either local or on some server somewhere.
Once you have data, e.g. SNP data from the next gen analysis, you can
use existing workflows to identify genes from sequences, expressions
rates, and biological pathways for each gene/protein. These are all
available from myExperiment.
The myGrid team has also been working on the annotation of next gen seq
SNP data using the Amazon cloud
(http://www.taverna.org.uk/introduction/taverna-in-use/genome-and-gene-expression/next-generation-sequencing/).
At the moment, this is closed beta testing, though funding has been
obtained for production of a working tool. More to come on this later in
the year.
Probably not want you wanted, but unfortunately I can't share what I
have at the moment. I can only suggest things to do yourself.
regards,
Paul.
On 31/05/2011 17:58, john Abraham wrote:
Dear Users,
I am trying to attempt to do analysis of new generation sequencing
data as part of my project. I request group to let me know if there
are any workflows that connect all applications from end to end to do
secondary and teritary analysis of New generation sequence data .
Any help in this or pointers is highly appreciated
Regards
John
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