Screening whole genome sequence data for mutations in regulatory regions of genes using galaxy

Question

[dchelimo]

I will be receiving whole genome sequence data in a coupe of weeks and my task will be to try and find mutations in non coding regulatory regions of the genes. I will have to compile maps of all the known places in the whole genome where the regulatory proteins of my gene of interest bind. I was wondering if Galaxy will be a good tool carrying out the exploration. And if so, is there a recommended pipeline doing the analysis. Any help would be highly appreciated.

[jotan]

There is a Biostars specifically for Galaxy. You might have more luck with your question there.

Answer 1

[Jennifer Hillman Jackson]

Hello,

I didn't find a post at Galaxy Biostars, but this tutorial should help you to learn about variant calling and downstream annotation in Galaxy. Modify the example tutorial to create a workflow that meets your specific analysis goals.

https://github.com/nekrut/galaxy/wiki/Diploid-variant-calling

Thanks, Jen, Galaxy team