Cell Ranger ATAC

methylpy — Python pipeline for whole-genome bisulfite sequencing (WGBS) methylation analysis. Trims adapters, aligns with Bowtie2, marks duplicates, and calls cytosine methylation in CpG, CHG, and CHH

2 shared topics • 2 shared operations

CUT&RUNTools 2.0 — end-to-end analysis pipeline for CUT&RUN and CUT&TAG chromatin profiling experiments. Handles adapter trimming (Trimmomatic), spike-in normalization, Bowtie2 alignment with size-sel

1 shared topic • 3 shared operations

ENCODE DCC ATAC-seq pipeline — ENCODE consortium-standard WDL/Cromwell pipeline (run via Caper) for processing bulk ATAC-seq data from FASTQ through alignment, deduplication, peak calling (MACS2), IDR

1 shared topic • 3 shared operations

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

2 shared topics • 1 shared operation

Tools for manipulating next-generation sequencing data stored in SAM/BAM/CRAM format, including sorting, indexing, and format conversion.

2 shared topics • 1 shared operation