Mercurial > repos > saket-choudhary > eqtl_tools
changeset 4:79ff64a36a31
Adding README
| author | Saket Choudhary<saketkc@gmail.com> |
|---|---|
| date | Thu, 20 Jun 2013 18:27:10 +0530 |
| parents | 54dddd7b44d0 |
| children | 5417d7cb27a0 |
| files | README |
| diffstat | 1 files changed, 28 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Thu Jun 20 18:27:10 2013 +0530 @@ -0,0 +1,28 @@ +This is a wrapper for a set of eQTL analysis tools. + +Though, currently only PANAMA is supported. +PANAMA takes in input as : + +$panama expression_data.csv snp_data.csv + +Where expression_data.csv is a Comma Separated Values file containing the gene expression data +in the following format: + + sample1, sample2, ..., sampleN + gene1 value , value , ..., value + gene2 value , value , ..., value + ... + geneN + +and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format: + + sample1, sample2, ..., sampleN + SNP1 value , value , ..., value + SNP2 value , value , ..., value + ... + SNPQ + +Make sure panama is installed and available on your path for all nodes. +Move the test-data files to your galaxy root test-data folder and +create a directory galaxy-central/tools/eqtl_tools and put +the panama_run.py and panama.xml files inside eqtl_tools directory.