Elementolab/ChIPseeqer Installation
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Contents |
ChIPseeqer Installation Instructions
Download
1. Download ChIPseeqer source code:
http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/ChIPseeqer-2.0.tar.gz
2. Untar the source code archive
tar xzf ChIPseeqer-2.0.tar.gz
Install
Read carefully the README file.
Follow the instructions described in the INSTALL file.
Files you will need
1. The gene annotation files.
| Species | File |
|---|---|
| human (hg19) | http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/hg19.tar.gz |
| human (hg18) | http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/hg18.tar.gz |
| mouse (mm9) | http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/mm9.tar.gz |
| drosophila (dm3) | http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/dm3.tar.gz |
| saccharomyces cerevisiae | http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/sacser.tar.gz |
Untar the annotation data inside the data directory.
cd data/ tar xzf hg18.tar.gz
2. The ENCODE datasets.
http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/Encode.tar.gz
Untar the encode datasets inside the data/NONGENIC_ANNOTATION directory.
cd data/NONGENIC_ANNOTATION/ tar xzf Encode.tar.gz
3. The genome fasta file.
Download the genome file of the species you want.
For example, for hg18:
- create a new directory:
mkdir hg18 cd hg18
- download genome (wget provides an easy way to do so, but you can also download the file manually and save it in hg18/):
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip
- unzip
unzip chromFa.zip
- concatenate all chromosome files:
cat *.fa > wg.fa
- erase chromosome files:
rm chr*.fa
4. The conservation scores.
PhastCons available at http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/
PhyloP available at http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/.
The easiest way to download the files is to use lftp.
For example:
lftp http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/placentalMammals/ mget *.gz quit
