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The data preprocessing pipeline for the VISION project (for human data)

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guanjue/vision_pipeline_human_hg19

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vision_pipeline_hg19_0526

Dependence:

Python/2.7

numpy, matplotlib, scipy

R

Input data

cell_list.txt in input folder
cell_list.txt
>>> head cell_list.txt 
H1
H2
CD34

mark_list.txt in input folder
mark_list.txt
>>> head mark_list.txt 
H3K4me1
H3K4me3
H3K27ac

replicate_list.txt in input folder
replicate_list.txt
>>> head replicate_list.txt 
R1
R2

run pipeline

The 1st parameter is the script folder of the pipeline; 2nd parameter is the input folder of the data
The 3rd parameter is the reference sample for across mark normalization (e.g. H3K4me3_H1_R1)
The 4th parameter is the reference cell type within mark normalization (e.g. H1)
The 5th parameter is the reference replicate id within mark normalization (e.g. R1)
time sh /storage/home/software/shared_pipeline/get_vision_human_rep.sh /storage/home/software/shared_pipeline/ /storage/home/data2run/test_data/ H3K4me3_H1_R1 H1 R1