I encountered the following error when running SMR in MacOX.
error can not open the file [Y] to read
This is my code:
./smr --bfile X --gwas-summary Y --beqtl-summary Brain-eMeta --out mysmr --thread-num 10
I believe the bfile X (the SNPs in my chromosome of interest) should be working alright, and the brain expression data file is from the downloads in the cnsgenomics.com website, so these two should be fine.
I guess then that indeed the problem is in the Y.txt which has the columns as they should be: SNP A1 A2 freq b se p N for the summary statistics of my chromosome of interest of a GWAS.
I have to say I'm a physician, not a bioinformatician, although I have been doing some computing. Thank you in advance:
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