nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) and assay for transposase accessible chromatin (ATAC-seq) data analysis.
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.
- Make BWA reference genome index (optional)
- Build BED reference based on GTF (optional)
- Build genome size table for bedToBam conversion (optional)
- FastQC for initial quality control of sequence reads
- TrimGalore! for adapter trimming
- BWA for alignment
- Samtools for post-alignment processing with and alignment statistics
- Picard MarkDuplicates for duplicate removal
- Count read statistics
- Phantompeakqualtools for NSC, RSC and strand-shift cross correlation plot
- DeepTools for paired-end fragment size distribution, fingerprint, reads distribution profile, sample pair-wise correlation, and PCA plot.
- MACS2 for peak calling
- MACS2 for saturation analysis (optional)
- Bioconductor ChIPpeakAnno for peak annotation
- MultiQC
The nf-core/chipseq pipeline comes with documentation about the pipeline, found in the docs/ directory:
These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. Written by Chuan Wang (@chuan-wang) and Phil Ewels (@ewels).