Mercurial > repos > saket-choudhary > eqtl_tools

comparison README @ 4:79ff64a36a31

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Adding README
author Saket Choudhary<saketkc@gmail.com>
date Thu, 20 Jun 2013 18:27:10 +0530
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3:54dddd7b44d0 4:79ff64a36a31
1 This is a wrapper for a set of eQTL analysis tools.
2
3 Though, currently only PANAMA is supported.
4 PANAMA takes in input as :
5
6 $panama expression_data.csv snp_data.csv
7
8 Where expression_data.csv is a Comma Separated Values file containing the gene expression data
9 in the following format:
10
11 sample1, sample2, ..., sampleN
12 gene1 value , value , ..., value
13 gene2 value , value , ..., value
14 ...
15 geneN
16
17 and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format:
18
19 sample1, sample2, ..., sampleN
20 SNP1 value , value , ..., value
21 SNP2 value , value , ..., value
22 ...
23 SNPQ
24
25 Make sure panama is installed and available on your path for all nodes.
26 Move the test-data files to your galaxy root test-data folder and
27 create a directory galaxy-central/tools/eqtl_tools and put
28 the panama_run.py and panama.xml files inside eqtl_tools directory.