This tool could help users to detect potential long-range effects of genome-wide SNPs on miRNA via super-enhancers in human osteoblast. Users could take a list of SNPs of interest as input, such as SNPs from GWAS summary results.
Use the follow command to download:
$ git clone https://github.com/WeiYang-BAI/Osteo-Fine-Mapp-SNP2SE2miRNA.git
Please run the follow command to to see the help message:
$ python ./FineMapp_SNP2SE2miRNA.py -H
Arguments:
-H/-h show this help message and exit.
-SNP The INDEPENDENT SNPs file, which consists of at least three tab-separated
columns: chromosome, position and P-value. Extra columns are allowed, but
the first two columns must be chromosome (1-22, X, Y) and position (in hg19).
-PCol Columns name of P-value in the SNP input file.
-outPrefix Prefix for output results.
An example is given, run it in the command line for details:
$ sh example.sh
Output:
-mapping.tsv, results of SNPs mapping to SEs.
-mappedSE-Bonferroni_sig.tsv, mapped SEs with P < 0.05/1224.
-Interaction_SE2miRNA.tsv, interactions between miRNA and SE.
-SE-interacted_pri-miRNA.txt, SE-interacted pri-miRNAs.
-SE-interacted_mature-miRNA.txt, mature miRNAs.
Note that the step of long-range interaction identification between Super-Enhancer and miRNA may take a while.