Instruction step 4: Run Metasoft (Meta-analysis software)

The last step in Meta-Tissue is to run software called Metasoft that performs meta-analysis. We already provided the script that runs Metasoft in Step 3. Hence, all users need to do is to execute the script. 

[output prefix].SNP.[start_SNP_index].metasoft.sh

1. If users parallelized MetaTissueMM in Step 3, then users also need to parallelize this step as well; run this shell script for each [start_SNP_index] file.

2. Running this script will generate a following output file:

[output prefix].SNP.[start_SNP_index].metasoft.output.txt.gz
Each line in output file contains p-value for each pair of SNP and gene expression from meta-analysis that combines information from multiple tissues; hence one p-value for each pair of SNP and gene expression pair. The first column indicates ID for a pair of SNP and gene expression, and ID is "[SNP ID]:[Probe ID]"
We recommend using results of meta-analysis FE and RE2. The p-value of FE is specified in 3rd column (PVALUE_FE) and the p-value of RE2 is specified in 4th column (PVALUE_RE2). If you did not specify "--no_mvalue" as an additonal option, the last T columns contain m-values (where T is the number of tissues). For more information on output of Metasoft, please refer to user's guide of Metasoft.

That's it! Congratulations on following all steps! If you have a trouble or a problem, please first check FAQ section. If your problem is not discussed, please contact me at jhsul at research dot bwh dot harvard dot edu.