Chip-seq Pipeline

This repository contains a pipeline for the analysis of the Transcription Factor and Histone Mark ChIP-seq data.

Motivation

The aim of this project is to create a standard pipeline that includes, metadata extraction, quality controls, data analysis and peak calling. This pipeline, receiving as input a list of GEO GSM ids and their corresponding factor (both Histone Marks and Transcription Factors), is able to automatically recognise the phred quality score, the sample's organism and discriminate single-end samples from paired end.

Pipeline summary

1. Fastq file download (parallel-fastq-dump)
2. Metadata Extraction (Entrez-Direct)
3. Raw read QC (FastQC)
4. Alignment (bowtie2)
5. Mark duplicates (SAMtools)
6. Filtering to remove:
   • reads mapping to blacklisted regions (SAMtools, bedtools)
   • reads that are marked as duplicates (SAMtool)
   • reads that are unmapped (SAMtool)
7. Evaluate sequencing alignment data (qualimap)
8. Calculate PCR bottleneck coefficient (PBC) & Non-Redundant Fraction (NRF) (pysam)
9. Call broad/narrow peaks (MACS2)
10. Present QC for raw read, alignment, peak-calling and differential binding results (MultiQC)