GenomicAlignments

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.

1 shared topic • 1 shared operation

FusionCatcher — tool for detecting somatic fusion genes, translocations, and chimeric transcripts from RNA-seq data. Identifies known and novel gene fusions in tumor and normal samples using multiple

1 shared topic • 1 shared operation

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

1 shared topic • 1 shared operation

RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i

1 shared topic • 1 shared operation

salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s

1 shared topic • 1 shared operation