Replicates Incorporation

소개

Automates the processing of biological replicates in bioinformatics workflows to ensure experimental reproducibility and data consistency. It operates in two primary modes: Pre-Peak Calling, which merges multiple BAM files and creates balanced pseudo-replicates for robust peak detection, and Post-Peak Calling, which applies Irreproducible Discovery Rate (IDR) analysis or consensus strategies to filter non-reproducible peaks. This skill is essential for generating high-confidence 'conservative' or 'optimal' peak sets from narrow or broad ChIP-seq and ATAC-seq data, providing a standardized path from raw alignments to validated signal peaks.

주요 기능

• Merging of multiple biological BAM files into pooled tracks
• Consensus peak merging for broad histone mark analysis
• Irreproducible Discovery Rate (IDR) analysis for narrow peak sets
• 2 GitHub stars
• Generation of balanced pseudo-replicates for robust peak calling
• Automated project directory initialization and standardized output architecture

사용 사례

• Combining more than two biological replicates to prepare for track generation
• Creating high-confidence consensus peak sets for histone mark studies
• Validating peak reproducibility between replicates using IDR