Generates normalized BigWig signal tracks from BAM files for ATAC-seq and ChIP-seq visualization.
Automates the process of converting filtered BAM alignment files into normalized BigWig signal tracks for high-quality genome browser visualization. This skill streamlines complex bioinformatics tasks such as RPM normalization, scaling factor calculation, and chromosome size generation. It specifically addresses domain-specific requirements by applying Tn5 offset corrections for ATAC-seq data while maintaining raw positions for ChIP-seq, ensuring that researchers can move quickly from alignment files to biological insights with standardized, ready-to-use output files.
Key Features
01Standardized project directory architecture and file organization
02Support for both ATAC-seq and ChIP-seq visualization protocols
03RPM (Reads Per Million) normalization for signal consistency
04Automated generation of chromosome size files and scaling factors
05Automatic Tn5 offset correction (+4/−5bp) for ATAC-seq tracks
062 GitHub stars
Use Cases
01Converting filtered BAM files into visualizable tracks for IGV or UCSC Genome Browsers
02Generating normalized signal tracks to compare multiple ATAC-seq samples
03Creating publication-ready BigWig files from ChIP-seq alignment data
