`finaletoolkit interval-end-motifs`¶

1. About¶

Measures frequency of k-mer 5' end motifs in each region specified in a BED file and writes data into a table.

The per-region counterpart of end-motifs. Instead of one 256-entry frequency vector for the whole genome, it produces one vector per genomic window, so nuclease preference becomes a spatial signal. Regions where the end-motif profile departs from the genome average point to locally different chromatin accessibility or nuclease activity.

In this pipeline the windows are the fixed-size intervals tiling the genome, built at the start of each run at the width given by --interval (default 1mb), so the output is a wide table: windows down the rows, 4-mer motifs across the columns.

2. As the pipeline runs it¶

finaletoolkit interval-end-motifs bams/{sample}.sorted.bam <ref2bit> <intervals> \
    -q <--mapscore> \
    -k 4 \
    -min <--fragment-minimum> \
    -max <--fragment-maximum> \
    -o interval_end_motifs/{sample}_endmotif_interval.tsv \
    -w <threads> \
    -v

2.1 Arguments¶

input_file

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

refseq_file

2bit reference sequence. value: the ref2bit file for the selected --genome build

Motifs are read from the reference rather than from the reads, so base-calling errors at fragment ends do not affect the tally.

intervals

Windows to tabulate motifs over. value: intervals/{genome}_{size}_intervals.bed, tiled from the selected build's reference FastA at the --interval width

-k

k-mer length. value: 4 — 256 motifs, matching end-motifs

-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)

Passed as -min/-max. FinaleToolkit still accepts -lo/-hi as deprecated aliases for these; the pipeline uses the current names.

-w, --workers

Worker processes. value: the step's threads from config/cluster.json (default 16)

Both strands are counted

-B, --single-strand would restrict the tally to one strand. The pipeline does not pass it, so both strands' 5' ends contribute — consistent with end-motifs. Note the flag name differs between the two subcommands: --single-strand here, --no-both-strands there, for the same -B short form.

3. Output¶

interval_end_motifs/{sample}_endmotif_interval.tsv — a table with one row per interval and one column per 4-mer motif, holding that motif's frequency within the interval.

This is the largest per-sample text output in the pipeline: genome-wide windows against 256 motif columns. At the default --interval 1mb that is a few thousand rows; a narrow width such as 5kb runs to hundreds of thousands. Its memory allocation is correspondingly the largest of the motif steps.

4. Controlling it¶

What	How
Fragment length window	`--fragment-minimum`, `--fragment-maximum`
Which windows	`--interval`, which sets the width the windows are tiled at
Reference sequence	the `ref2bit` entry for the selected build
Threads / memory / walltime	the `interval_end_motifs` entry of `config/cluster.json`

"interval_end_motifs": {
    "threads": 16,
    "mem": "96G",
    "time": "08:00:00",
    "partition": "norm"
}

The 96 GB allocation reflects the size of the interval × motif table held in memory while it is assembled. If this step is killed for exceeding memory, either raise mem or pass a coarser --interval width.

5. Requires¶

ref2bit and reference_fa (which the interval BED is tiled from) for the selected genome build. Both bundled builds provide both.

end-motifs — the same measurement genome-wide
mds — motif diversity score, computed from the genome-wide vector

finaletoolkit interval-end-motifs¶