         #####  Contact  #####
Date: Oct. 30, 2013
This collection of scripts(workflow) was developed by the 
Bioinformatics team at Mayo Clinic Rochester, MN

Please email questions to:
Yan, Huihuang, Ph.D. <Yan.Huihuang@mayo.edu>
Moore, Raymond M. <Moore.Raymond@mayo.edu>



##### Installation instructions  ######

Example: install tools, except BedTools
chipseq_wf/install.sh --dir /data2/bsi/RandD/m088378/sandbox/ --skip-bedtools -v




###### Reference Manifest ######
test_samples.tar.gz (282M)
 - TestDataSet/GSM798440a_MCF7_Input_q15.chr1.chr2.1M.fastq.gz
 - TestDataSet/GSM798424_MCF7_2_IP_q15.chr1.chr2.1M.fastq.gz
 - TestDataSet/GSM798423_MCF7_1_IP_q15.chr1.chr2.1M.fastq.gz
 - TestDataSet/GSM798425_MCF7_3_IP_q15.chr1.chr2.1M.fastq.gz
 - TestDataSet/GSM798440c_MCF7_Input_q15.chr1.chr2.1M.fastq.gz
 - TestDataSet/GSM798440b_MCF7_Input_q15.chr1.chr2.1M.fastq.gz

human_references.tar.gz (1.2G)
 - references/track_color_list.txt
 - references/IGV_Setup.pdf
 - references/annotation/
 - references/annotation/hs.GO_annotation.txt
 - references/annotation/Hg19.great2.0.genes.v2.txt
 - references/annotation/hg19.non_gap.bed
 - references/allchr.fa
 - references/hg19.genome
 - references/TSS_112.in
 - references/hg19.refGene
 - references/ucsc_refflat_hg19_2011-01-24.txt
 - references/ChIP-Seq_workflow_summary.doc
 - references/hg19.contig.sizes
 - references/genome_table.human.hg19.txt

mouse_references.tar.gz (1.1G)
 - references/track_color_list.txt
 - references/genome_table.mm10.txt
 - references/IGV_Setup.pdf
 - references/mm10.genome
 - references/annotation/
 - references/annotation/mm10.non_gap.bed
 - references/annotation/Mm.GO_annotation.txt
 - references/annotation/Mm10.great2.0.genes.v2.txt
 - references/refFlat.txt
 - references/genome.fa
 - references/ChIP-Seq_workflow_summary.doc

 
 