Peakachu

MACS2/MACS3 — Model-based Analysis of ChIP-Seq for identifying transcription factor binding sites and histone modification enrichment from ChIP-seq, ATAC-seq, and CUT&Tag data. Provides peak calling (

2 shared topics • 1 shared operation

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

2 shared topics • 1 shared operation

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format, demultiplexing sequencing runs by index sequences, or trimming adapters from short-read data. Handles HiSeq, MiSeq, NextSeq,

2 shared topics

BEDTools — Swiss-army knife for genome arithmetic on genomic intervals. Provides intersect, merge, subtract, complement, closest, window, coverage, genomecov, slop, flank, sort, groupby, getfasta, mas

2 shared topics

pygenometracks -- Python program and library for plotting publication-quality genome browser tracks. Generates highly customizable visualizations of bigwig, BED, GTF, bedgraph, Hi-C matrices, links/ar

2 shared topics