guanjue / gtex_pipeline_hg38_0601

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

gtex_pipeline_hg38_0601

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