CREB3-ChIP-Seq-Workflow is a reproducible and simple pipeline to analyze ChIP-seq data targeting the transcription factor CREB3. Designed for a human genome (GRCh38/hg38) context, automatized for:
Mapping Statistics and Quality Control: Calculates mapping quality and multi-mapping rates for ChIP and control input samples using samtools. Filters out low-quality and non-uniquely mapped reads.
Peak Calling: MACS2 to identify transcription factor binding sites. Multiple replicates are analyzed independently and jointly
Blacklist Filtering: Employs bedtools to eliminate artifactual peaks by excluding ENCODE blacklisted genomic regions, ensuring peak reliability.
Reproducibility Assessment: Identifies overlapping peaks between replicates within a 100 bp window to assess replicate concordance.
Politecnico di Milano - University of Milan