Analytical tools and pipelines

Pipelines for processing and analyzing data from epigenomic assays and integrating with genetic association data

 

Epigenome database

Instructions for deploying and depositing data into epigenome database DGA based on ENCODE:

DGA/ 

 

ATAC-seq

Process bulk (i.e. non-single cell) ATAC-seq data:

bulk_ATAC-seq/bulk_ATAC-seq_pipeline.py 

ENCODE ATAC-seq pipeline:
https://github.com/ENCODE-DCC/atac-seq-pipeline

 

ChIP-seq

Process TF or histone modification ChIP-seq data:

ChIP-seq/ChIP-seq_pipeline.py  

ENCODE ChIP-seq pipeline:
https://github.com/ENCODE-DCC/chip-seq-pipeline2

 

RNA-seq

ENCODE RNA-seq pipeline:
https://github.com/ENCODE-DCC/rna-seq-pipeline

 

CUT&RUN

Process TF or histone modification CUT&RUN data:

CUTNRUN/cut_and_run_pipeline.py  

 

PLAC-seq

Process PLAC-seq/HiChiP data.

PLAC-seq/MAPS_pipeline.py

 

Single nuclear ATAC-seq

Process single nuclear ATAC-seq (snATAC-seq data)

Pipeline used for human lung snATAC-seq data in Wang, Chiou et al bioRxiv:

snATAC_seq/lung_snATAC_pipeline.py 

SnapATAC:
https://github.com/r3fang/SnapATAC