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WASP (Weight And SNP-based Pipeline) corrects allele-specific mapping bias in RNA-seq and ChIP-seq by SNP-masking reads that overlap heterozygous variants, remapping them, and filtering those that shi
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Install the MCP server or CLI to instantly fetch WASP documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/wasp
AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome
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
3 shared topics • 1 shared operation
BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace
2 shared topics • 2 shared operations
Use when performing precision HLA class I typing from NGS data with OptiType. Covers read mapping to HLA reference with YARA, Integer Linear Programming allele calling at 4-digit resolution for HLA-A,
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