Mercurial > repos > saketkc > eqtl_tools

annotate README @ 4:eb7d9fdf8ec9 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix structure
author Saket Choudhary <saketkc@gmail.com>
date Tue, 09 Jul 2013 14:45:12 +0530
parents 832a77c2ea1d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
1
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
2
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
3 This is a wrapper for a set of eQTL analysis tools.
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
4
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
5 Though, currently only PANAMA is supported.
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
6 PANAMA takes in input as :
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
7
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
8 $panama expression_data.csv snp_data.csv
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
9
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
10 Where expression_data.csv is a Comma Separated Values file containing the gene expression data
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
11 in the following format:
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
12
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
13 sample1, sample2, ..., sampleN
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
14 gene1 value , value , ..., value
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
15 gene2 value , value , ..., value
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
16 ...
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
17 geneN
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
18
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
19 and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format:
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
20
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
21 sample1, sample2, ..., sampleN
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
22 SNP1 value , value , ..., value
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
23 SNP2 value , value , ..., value
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
24 ...
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
25 SNPQ
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
26
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
27 Make sure panama is installed and available on your path for all nodes.
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
28 Move the test-data files to your galaxy root test-data folder and
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
29 create a directory galaxy-central/tools/eqtl_tools and put
832a77c2ea1d Fix the file organisation
Saket Choudhary <saketkc@gmail.com>
parents:
diff changeset
30 the panama_run.py and panama.xml files inside eqtl_tools directory.