MatrixeQTL2LocusZoom
Script will use three parameters as inputs, 1) Gene ID from ENSEMBL annotation, 2) chromosome number where the gene is located 3) eQTL file from matrixeQTL and generate output for visualization with LocusZoom Plot containing rsIDs and p-values as columns 1 and 2.
Install / Use
/learn @milospjanic/MatrixeQTL2LocusZoomREADME
matrixeQTL2LocusZoom
This script will take three parameters as inputs, 1) Gene ID from ENSEMBL annotation, 2) chromosome number where the gene is located 3) eQTL file from matrixeQTL in the following format:
<pre> head AOR_TCF21_eqtls.txt "snps" "gene" "statistic" "pvalue" "FDR" "beta" "6:134214525" "ENSG00000118526.6" -8.00604105843143 8.03916943247416e-15 8.27596273928866e-13 -0.472596606956573 "6:134226147" "ENSG00000118526.6" -7.76939299996685 4.35609034489325e-14 4.1908757955211e-12 -0.453463080643677 "6:134209837" "ENSG00000118526.6" -5.91258104036461 6.16525172030328e-09 3.6491797333611e-07 -0.434239358522576 "6:134215779" "ENSG00000118526.6" -5.4626188984354 7.33863755697273e-08 3.7776937355882e-06 -0.335590058154907 "6:134215155" "ENSG00000118526.6" -5.46040034813125 7.42581108817843e-08 3.82004547528766e-06 -0.335842843000443 "6:134219229" "ENSG00000118526.6" -5.4546658391212 7.6558233417211e-08 3.93297487388231e-06 -0.335279178823917 "6:134204247" "ENSG00000118526.6" -5.39357457171944 1.05780776839588e-07 5.3217557036282e-06 -0.397099262828128 "6:134202690" "ENSG00000118526.6" -5.37526674283146 1.16474164877705e-07 5.8287500535325e-06 -0.398573998449558 "6:134184272" "ENSG00000118526.6" -4.85278383205625 1.61954736331598e-06 6.82414031433209e-05 -0.387056671918765 </pre>#Executing script Download dbSNP142 summary file, snp142.cut_tab.gz, from https://stanfordmedicine.box.com/s/2scotvvcppu487yy3okx45k4awow0eo0
Unzip dbSNP142 file, snp142.cut_tab.gz
Download matrixeQTL2LocusZoom.sh
<pre> chmod 755 matrixeQTL2LocusZoom.sh ./matrixeQTL2LocusZoom.sh ENSG00000118526 6 AOR_TCF21_eqtls.txt </pre>#Output
Output file will be named according to ENSEMBL geneID and have extension .eQTL.rsIDs, and contain rsIDs and p-values as columns 1 and 2
<pre> head ENSG00000118526.eQTL.rsIDs rs3777810 0.395091136884783 rs159417 0.451121029045717 rs74786004 0.486213935779129 rs159418 0.309231443202701 rs73559684 0.653963276491878 rs159419 0.433273033090162 rs149078286 0.176463218466757 rs181411522 0.707869402571322 rs3777811 0.830651265778997 rs34925767 0.761642570067226 </pre>Plotting in LocusZoom (example of cis-eQTLs for TCF21 gene on chromosome 6):
