Sequence-data-analysis-for-noise-control

The source code for the paper "Quantitative Control of Noise in Mammalian Gene Expression by Dynamic Histone Regulations".

If you want to run the code, please read the following descrptions and pay attention to the file path. The file path in the code should be modified according to your file path.

build_reference

It includes the code to build the HeLa-AB1 reference genome which for ATAC-seq, ChIP-seq and scATAC-seq data processing. The metadata directory includes some input and intermediate files which are used in the code.

Procedure

step1: run the code in get_reference.sh

ChIP-seq

It includes the code to process the ChIP-seq data.

Procedure

step1: run the code in chip_analysis.sh

step2: run the code in calculate_depth.py

ATAC-seq

It includes the code to process the ATAC-seq data.

Procedure

step1: run the code in atac_analysis.sh

step2: run the code in calculate_depth.py

scATAC-seq

It includes the code to process the scATAC-seq data. The metadata directory includes some input and intermediate files which are used in the code.

Procedure

step1: run the code in scatac_analysis.sh

step2: run the code in calculate_depth.py

scRNA-seq

It includes the code to process the scRNA-seq data. The metadata directory includes some input and intermediate files which are used in the code.

Procedure

step1: run the code in new_ref.sh

step2: run the code in 10x_scRNA.sh

step3: run the code in qc.R

step4: run the code in combine_repeat.py

step5: run the code in F9_scRNA_analysis.m and Hela_scRNA_analysis.m