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eskederks / eMAGMA-tutorial

A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.
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Reference genome build file #10

Open rezarahman12 opened 6 months ago

rezarahman12 commented 6 months ago

Dear eMAGMA team, I've found that the link provided to download the Genome1000 reference file is not working. Could you please share African ancestry genome 1000 reference file so that I can run eMAGMA? I appreciate your time and help.

Kind regards Reza QBI, UQ

eskederks commented 6 months ago

Hi Reza, This is Zac's response. "The African sub-population reference data for 1000G can be downloaded from MAGMA website (https://cncr.nl/research/magma/) (under “reference data”). But I don’t think it’s a good idea to run eMAGMA on samples with non-European ancestry since the eQTL data was derived from GTEx European-only samples. We would need to create new ancestry-specific annotation files. This is a limitation of the method". We might look into this in the future to allow this method to be used for other ancestries.