Tag: peak-calling
CUT/CUT Peak Calling Pipeline
This tool executes a comprehensive Nextflow pipeline for processing CUT or CUT FASTQ data. It handles alignment, spike-in normalization, and generates peak calls using SEACR or MACS2, producing normalized signal tracks and genomic peaks.
ENCODE ChIP-seq Analysis Pipeline for Peak Calling
This skill executes a complete, standards-compliant ChIP-seq workflow, processing raw FASTQ files through alignment, MACS2 peak calling, and IDR analysis. It generates comprehensive peak sets and signal tracks, adhering to ENCODE guidelines…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility Analysis
This skill executes the comprehensive ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and filtering. It generates high-quality peak calls and signal tracks suitable for detailed chromatin acces…
Aggregate histone mark peaks across multiple studies
This skill constructs comprehensive histone mark maps by aggregating narrowPeak data from multiple ENCODE experiments, donors, and labs into a single union peak set. It handles complex data quality steps, including ENCODE blocklist filterin…
CUT and CUT Processing Pipeline
Executes a Nextflow-based pipeline for processing CUT and CUT data from FASTQ files to peaks and signal tracks. The workflow incorporates spike-in normalisation and SEACR peak calling for high-resolution chromatin profiling.
ENCODE ChIP-seq Processing Pipeline
This Nextflow-based pipeline executes the complete ENCODE ChIP-seq processing workflow, transforming raw FASTQ files into peaks and signal tracks. It handles quality control, alignment, peak calling with MACS2, and IDR analysis using Docker…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility
This tool executes the full ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and rigorous filtering. It generates nucleosome-free peaks and signal tracks following established ENCODE standards.