Hello everyone!
We work on GWAS, mainly, and we need to get informations about SNPs like:
I want to use ENCODE data for this but there is a lot of different data and many files.
Have you any advice for me which will help to get datas from them?
Which file do you use? Which tool (provided by UCSC or example of SQL request...)?
Do you use data other than ENCODE's (for example for the binding motifs)?
Thank you in advance.
Best regards, Nolwenn.
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written
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Nolwenn Lavielle
did you try:
haploreg: http://www.broadinstitute.org/mammals/haploreg/haploreg.php
or
regulomeDb: http://regulome.stanford.edu
?
Hi Pierre Lindenbaum
I also have some questions want to get your guidance. If I have genome resequencing SNPs located in intergenic regions and I want to know whether are they in cis-regulatory element or not, what should I do? Do you know some approaches to deal it?
no, and you should ask this as a new question.
Ok, Thanks Pierre Lindenbaum. I have asked it as a new question. How to locate the intergeneic SNPs in cis-regulatory element
I am also investigating on HaploReg but some of those datas seems to be calculated, in particular for the "Regulatory motif altered". I wonder if ENCODE provide this kind of informations too?
I had not try RegulomeDB, thanks for the reference! :)
I am confused. I was not sure if I had to comment or answer, now I am aware about this subtility. Thank you very much!
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