UCL-BLIC/chipseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-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)
- FastQC
- TrimGalore!
- Align with BWA
- Samtools sort, index, stats & convert to BED
- Samtools idxstats
- Picard MarkDuplicates
- Create bigwigs
- Count read statistics
- PhantomPeakQualTools
- SPP: Calculate NSCRSC and cross correlation
- DeepTools bamPEFragmentSize, plotFingerprint, bamCoverage, multiBamSummary, plotCorrelation, plotPCA
- NGSplot
- MACS2 peak calling
- Saturation analysis
- ChIP peak annotation
- MultiQC
The UCL-BLIC/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).