domains / families / science / bio-workflows-chipseq-pipeline

bio-workflows-chipseq-pipeline

separate

End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.

When to use

• processing ChIP-seq data
• QC and trimming with fastp
• alignment with Bowtie2
• BAM processing and duplicate removal
• peak calling with MACS3
• QC metrics calculation
• peak annotation with ChIPseeker

Skill page

Source