Roadmap Epigenomics

bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.

3 shared topics • 1 shared operation

Use when working with Gviz, the Bioconductor R package for plotting genomic coordinates, annotations, signal tracks, read alignments, and sequence context in genome-browser-style figures. Covers core

2 shared topics • 2 shared operations

Use when working with Rsubread, the Bioconductor R package for read alignment, exon junction discovery, feature counting, long-read mapping, annotation flattening, and alignment QC. Covers buildindex(

2 shared topics • 2 shared operations

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

2 shared topics • 1 shared operation

Use when working with pybedtools — pybedtools — Python interface to BEDTools

2 shared topics • 1 shared operation