Question: Helicos sequencing data
gravatar for Laura.Collins
3.6 years ago by
Laura.Collins0 wrote:

I've downloaded a set of SRA files containing Helicos sequencing data.  Are there any tools on Galaxy that are suitable to for Helicos data?

rna-seq forum galaxy • 866 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by Laura.Collins0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I believe that Tmap will work with this datatype. A few wrapper options are in the Tool Shed for use in a local or cloud Galaxy

However, it would be optimal to find a publication that covers what you want to do (or close to it), then search for the same or similar Galaxy wrapped tools, to build up a full protocol. There are proprietary tools available, but that is probably a choice you will want to make after seeing what else is available in the public domain (that are still usable). The original company is long gone, but it was picked up by another that is still active. And I very much I dislike saying this, but google will point to more details that I can list out here about current options and the technology history. Legacy tools seem to be maintained in various places, just from a quick scan.

Once you find what you want to use - if not Tmap, or you want to use additional analysis tools to round out the protocol - nearly any bioinformatics tool can be wrapped for use in Galaxy. If you identify tools that you want to use that are not already wrapped, those could be wrapped and used in a local/cloud, if you have resource available to do that yourself or in your research group.

Seqanswers also has a forum dedicated to this technology - but much is several years old. Still, it is worth look, if you have not already reviewed.

Others are welcome to comment/add more info.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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