The snp allele information in the file called 'Genome wide significant eQTL snp-feature pairs'

LieberInstitute / brainseq_phase2

BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium

http://eqtl.brainseq.org/

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The snp allele information in the file called 'Genome wide significant eQTL snp-feature pairs' #31

Closed Lee211 closed 4 years ago

Lee211 commented 5 years ago

i cannot find the snp allele information (i.e. A1/A2, or ref/alt) in the file called 'Genome wide significant eQTL snp-feature pairs'. Are these data available?

lcolladotor commented 4 years ago

Hi @Lee211,

Sorry that I missed this. We have that information in another file described in https://github.com/LieberInstitute/brainseq_phase2/tree/master/browser#snp-information. Let me check what's the best way for us to share it.

Best, Leonardo

lcolladotor commented 4 years ago

Hi @Lee211,

In https://github.com/LieberInstitute/brainseq_phase2/commit/48edebd6b5c739aa313dcd74878af94fb7d1b756 I updated our documentation about these files. Also, the SNP annotation file is available here which has the columns newref (lower case for newRef) and newcount (lower case for newCount) which are the columns you wanted. You can match the different tables using the snp column from the files in SupplementaryTable15_eQTL.tar.gz and the SNP annotation table.

Best, Leo