Hi Sultana,

On 6/21/13 8:02 AM, sultana tahiri wrote:

Hello,

We are starting a project in our laboratory which aims to annotate a given set of SNPs lying in non-coding DNA from GWAS studies.
We would like to have the most comprehensive view of those non-coding SNPs putative and validated functions.
We've already been through publications about Galaxy and GalaxyENCODE, we also been searching for similar request on the FAQ but found no similar request dated from 2013. We would like to know about the latest add to Galaxy, as we've seen that part of the BEDtools have been integrated to Galaxy for example.

Our question is:

-What Tools available in Galaxy would take as an input a list of non-coding SNPs (or DNA regions) identified in our GWAS studies and return annotations of those SNPs (annotations such as histones modification, transcription factor binding, and other non-coding DNA features around those SNP) ?

Tools in the group " Phenotype Association" tend to focus on exome annotation, but you can have a look and see if any are a fit. SnpEff down in the NGS tools is most likely a better fit and is one of the newer additions. If running on a larger genome, a cloud or scaled up local Galaxy would be recommended:
http://usegalaxy.org/cloud

We haven't found a searching option on Galaxy that would allows us to look for tools by keywords related to their function or purpose. We assumed that we might have missed something, thank you for letting us know if there were such searching options.

Any of the bed/interval/BAM intersection tools (found by using a keyword search at the top of the tool panel, such as "interval" or "BAM") can be used to compare your data with other annotation mapped to the same reference genome that you locate and upload (without a specialized tool, these just use coordinates). Tools can also be search for in the Tool Shed (log in to have full access to all annotation/features).
http://toolshed.g2.bx.psu.edu/

Hopefully one of these options works out for you,

Jen
Galaxy team

Thanks you very much for your time,

Kind regards,

Sultana

The Center for Neurogenomics and Cognitive Research
De Boelelaan 1085
1081 HV Amsterdam
The Netherlands

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