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README 2016-01-27 1.2 kB
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variables.txt 2016-01-27 757 Bytes
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LnCaP1_ATCACG_L004_R2_.fastq.gz 2015-05-29 282.6 MB
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LnCaP1_ATCACG_L004_R1_.fastq.gz 2015-05-29 277.1 MB
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site_info.csv 2015-05-29 3.0 kB
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human_assembled_genome_GRCh38.fa.gz 2015-05-29 775.6 MB
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Totals: 6 Items   1.3 GB 0 
############################

3C-MTS example data
########################## 

Specie: human
Reference genome sequence: Assembly GRCh38
cell line: LnCAP prostate cancer cell line 

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

1. uncompress fastq files (R1 and R2) 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_3CMTS.pl ./result/variables.txt

Note: This dataset is only an example after removing paired-end read sequences without junction DNAs, and test passed by 3C-analyzer v1.2
#############

Citation: 

Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Wang L. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet. 2015 Jan 1;24(1):154-66. doi: 10.1093/hmg/ddu426. Epub 2014 Aug 22.


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