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Contents 1 ChIPseeqer Installation Instructions 1.1 Download 1.2 Install 1.3 Files you will need

ChIPseeqer Installation Instructions

Currently ChIPseeqer is available as source code only (you need to compile). Binaries will be made available soon.

Download

Download ChIPseeqer source code

1. Unstable, latest working version

(download the code from our repository)

The latest code available at the svn includes the programs for the NMF-regression modeling of protein complexes (send email to Jenny for more information -eug2002 AT med.cornell.edu-)

 svn checkout --username guest --password email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/ChIPseeqer/trunk ChIPseeqer/

2. Stable versions

(recommended for new users)

Version 2.1 (supports hg19, hg18, mm10, mm9, rn4, dm3, zv9 and yeast genomes)

Bugs fixes and several updates (see http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_versions)

http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/ChIPseeqer-2.1.tar.gz
tar xzf ChIPseeqer-2.1.tar.gz

Version 2.0 (only supports hg18, mm9, dm3 and yeast genomes)

http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/ChIPseeqer-2.0.tar.gz
tar xzf ChIPseeqer-2.0.tar.gz

Install

Read carefully the README file.

Follow the instructions described in the INSTALL file.

Known installation issues

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 (mm10)	http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/mm10.tar.gz
mouse (mm9)	http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/mm9.tar.gz
rat (rn4)	http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/rn4.tar.gz
drosophila (dm3)	http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/dm3.tar.gz
zebrafish (zv9)	http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/zv9.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 hg19.tar.gz

2. The ENCODE datasets.

http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/Encode_hg18.tar.gz http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/Encode_hg19.tar.gz

Untar the encode datasets inside the data/NONGENIC_ANNOTATION directory.

cd ChIPseeqer-2.1/data/NONGENIC_ANNOTATION/

tar xzf Encode_hg18.tar.gz tar xzf Encode_hg19.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

Old version of installation instructions