I encountered several problems when learning SMR(http://cnsgenomics.com/software/smr/#DataManagement), as follows:
When I prepared BESD format data, It requires the preparation of a probe-related data(such us myeqtl.epi file-- [1 probe1001 0 924243 Gene01 +]...). Unfortunately, the expression data I used dataset was RNA-seq generated without the probe information. Could you please tell me what should I do?
I choose method 4(Make a BESD file from eQTL summary data in PLINK-qassoc output format) to make a BESD file, I am confused about if need to split plink eQTL results and genotype data(.bim format) into individual chromosomes(chr1-chr22)? I can't find a clear answer on the description SMR website.
When I prepared BESD format data used method 4(Make a BESD file from eQTL summary data in PLINK-qassoc output format), I also need to prepare an input file--my.flist (Chr ProbeID GeneticDistance ProbeBp Gene Orientation PathOfEsd PathOfBim). My question is do these two parameter paths(PathOfEsd,PathOfBim) need absolute paths?
for 1). Use the chromosome of the gene as the probe chromosome. SMR uses a window centered around the probe as the cis-region. The default value is 2Mb. General speaking, gene length is relatively smaller than this size. It would not affect the SMR result significantly by setting the start position, the middle position, or the end position of the gene as the relevant probe position. You may set the 5th and the 6th column of .epi file as NA
for 2). You can use the .bim which contains chr1-chr22. Or split the .bim into 22 files and use the one relevant to the eQTL summary data in PLINK-qassoc output format. As long as the SNP in the eQTL summary data in PLINK-qassoc output format can be found in the following .bim file.
for 3). Absolute path and relative path are both accepted.