CLIP-seq Peak Calling

CLIPper (Recommended)

# Basic peak calling
clipper \
    -b deduped.bam \
    -s hg38 \
    -o peaks.bed \
    --save-pickle

# With FDR threshold
clipper \
    -b deduped.bam \
    -s hg38 \
    -o peaks.bed \
    --FDR 0.05 \
    --superlocal