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variables.txt 2016-01-27 1.4 kB
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README 2016-01-27 880 Bytes
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sample_info.csv 2015-05-29 68 Bytes
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site_info.csv 2015-05-29 72 Bytes
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SRR550183_hba_FL_487508.fastq.gz 2015-05-29 45.0 MB
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SRR550184_hba_FB_656.fastq.gz 2015-05-29 10.6 MB
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mouse_mm9_NCBI_build37_2007.fa.gz 2015-05-29 747.4 MB
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Totals: 7 Items   803.1 MB 0 
############################

4C-seq example data (GSE40420)
########################## 

Specie: mouse
Reference genome sequence: Assembly mm9


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#Guideline of running example 4C-seq data 
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make sure the installation of 3C-analyzer and bowtie2 before running example data.

1. uncompress fastq files (Fetal brain and fetal liver) and copy them in the directory known as ./raw_data
2. copy the files sit_info.csv and variables.txt into the directory ./result
3. copy the genome references fasta file into the directory ./references
4. run this command line :
	perl main_4C.pl ./result/variables.txt

#############

Citation: 

GSE40420

    van de Werken HJ, Landan G, Holwerda SJ, Hoichman M et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 2012 Oct;9(10):969-72. PMID: 22961246



Tiezheng Yuan 20150520
Source: README, updated 2016-01-27