finaletoolkit cleavage-profile¶

1. About¶

Calculates cleavage proportion over intervals defined in a BED file.

Measures, at each base, the proportion of overlapping fragments that end there — that is, how often nucleases cut at that exact position. Where WPS infers nucleosome protection from fragments spanning a window, cleavage profile reads the cut sites directly.

Around a transcription start site the profile shows depleted cleavage where nucleosomes sit and elevated cleavage in the exposed linker regions, giving a complementary view of the same chromatin structure at finer resolution.

2. As the pipeline runs it¶

finaletoolkit cleavage-profile bams/{sample}.sorted.bam <tss> <chrom_sizes> \
    -o cleavage_profile/{sample}_cleavage_profile_tss.bw \
    -l <--left-tss-flank> \
    -r <--right-tss-flank> \
    -q <--mapscore> \
    -min <--fragment-minimum> \
    -max <--fragment-maximum> \
    -w <threads> \
    -v

2.1 Positional arguments¶

input_file

The analysis BAM. value: bams/{sample}.sorted.bam

interval_file

Sites to profile around. value: the tss file for the selected --genome build — individual TSS positions

chrom_sizes

Chromosome name and length table. value: the chrom_sizes file for the selected build

Defines the coordinate space of the output bigWig and bounds the flanked intervals so they cannot run off the end of a contig.

2.2 Options¶

-l, --left

Base pairs subtracted from each site's start coordinate. value: --left-tss-flank (default 2000)

The TSS file gives point positions, so a region has to be built around each one before a profile can be computed. This extends it upstream.

-r, --right

Base pairs added to each site's stop coordinate. value: --right-tss-flank (default 2000)

Extends the region downstream. With both defaults, each profile spans ±2 kb of the TSS — enough to cover the nucleosome-depleted region and the flanking nucleosome array.

Asymmetric flanks are allowed

--left-tss-flank and --right-tss-flank are separate options, so the window need not be symmetric. Widening only --right-tss-flank extends the profile further into the gene body, where the downstream nucleosome array is most regular.

-q, --quality-threshold

Minimum mapping quality. value: --mapscore (default 20)

-min, --min-length / -max, --max-length

Fragment length window. value: --fragment-minimum / --fragment-maximum (defaults 50 / 500)

Unlike wps, this analysis does honor the pipeline's fragment-length options, so the full 50–500 bp range contributes cut sites by default. Passed as -min/-max; FinaleToolkit also accepts -lo/-hi as deprecated aliases.

-w, --workers

Worker processes. value: the step's threads from config/cluster.json (default 24)

3. Output¶

cleavage_profile/{sample}_cleavage_profile_tss.bw — a bigWig of the per-base cleavage proportion across every flanked TSS window.

It is also aggregated across all windows by agg-bw into cleavage_profile/{sample}_cleavage_profile_aggr.wig, which is the more interpretable product: averaging over tens of thousands of TSSs is what makes the nucleosome periodicity emerge from what is a sparse signal at any single site.

4. Controlling it¶

"cleavage_profile": {
    "threads": 24,
    "mem": "96G",
    "time": "2-00:00:00",
    "partition": "norm"
}

This is the most expensive analysis step in the pipeline — 96 GB and a two-day walltime — because it evaluates every fragment endpoint against every base of every flanked TSS window. Widening the flanks increases its cost proportionally.

5. Requires¶

tss, tss_interval and chrom_sizes for the selected genome build. (tss_interval is needed by the aggregation step that consumes this output, which is why the workflow gates both on all three.) Both bundled builds provide them.