ROSE

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.

2 shared topics • 1 shared operation

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

MEME Suite — motif-based sequence analysis toolkit for de novo motif discovery (MEME, STREME), motif enrichment testing (AME, SEA, CentriMo), motif scanning (FIMO, MAST, MCAST), motif comparison (Tomt

2 shared topics • 1 shared operation

Use when working with phantompeakqualtools — phantompeakqualtools (spp)

2 shared topics • 1 shared operation

Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m

2 shared topics • 1 shared operation