README.md

CHIPseq Manual

Version 1.0.6

May 31, 2019

BICF ChIP-seq Pipeline

Introduction

BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at BICF at UT Southwestern Department of Bioinformatics.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that supports Nextflow.

Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.