Full reference for every rnamotifs flag, grouped by role. See How the algorithm works for the concepts behind them.
Required
Flag
Meaning
input_file
Positional: the splicing-change file (Input Format), or an rMATS file with --from-rmats.
-n, --name
Run name; becomes the results sub-folder and plot title.
-g, --genome
Reference assembly: hg19, hg38, mm9, mm10, mm39. The matching genome must be downloaded (genomes/).
Clustering — what counts as a motif cluster
Flag
Default
What it controls
When to change
-w, --half-window
15
Half-width hw (bp) for clustering motif copies; copies within ±hw join one cluster. In paper notation this is the clustering window n = 2·hw (--n is an alias: --n 30 ⇔ -w 15). Larger → looser, longer-range multivalency.
Increase to capture dispersed motif arrays; decrease for tight local clusters. The MaRs sweep tries hw ∈ {5, 15, 25, 35} (n ∈ {10, 30, 50, 70}).
-m, --min-height
4
Minimum number of motif copies stacked within a window to call a cluster. Higher → stricter.
Lower (2–3) for sparse motifs / small exon sets; raise for very abundant motifs.
-p, --pth
0.5
Percentage threshold used when binarising cluster occupancy along the map.
Rarely changed; leave at default unless reproducing a specific protocol.
Region geometry — where you look
Flag
Default
What it controls
-e, --enrichment-window
30
Enrichment window ew (bp; paper notation e) over which positional enrichment is aggregated. Larger → smoother, broader signal. The MaRs sweep tries {30, 50, 100, 200, 300}.
--in-exon
30
How far (bp) into the exon the analysed region extends from each splice site.
--in-intron
300
How far (bp) into the intron the analysed region extends from each splice site.
--event-type
SE
SE (skipped exon) or 🚧 RI (intron retention — work in progress, see below).
hw (paper n = 2·hw) and ew (paper e) are the two parameters most worth tuning — they trade sensitivity vs specificity. There is no universal optimum; the MaRs discovery mode grid- or Bayes-searches them per RBP.
Statistics — how strict the filter is
Flag
Default
What it controls
-b, --bootstraps
10000
Bootstrap iterations for the empirical-FDR null. 1000 is the practical setting (fast; floor ≈ 10⁻³). 10000 is ~10× slower for a lower floor that rarely changes the called set.
--p-fisher
0.1
Fisher's-exact p-value threshold for regulated-vs-control enrichment.
--p-empirical
0.00005
Empirical p-value threshold from the bootstrap null. Only reachable with a large -b; with -b 1000 use a looser value such as 0.01.
-k, --kmer-size
4
Motif length. 4 (tetramers) is the validated default. 5/6 enumerate exponentially more, sparser motifs and generally reduce discriminability at higher cost.
Performance & plotting
Flag
Default
Meaning
-c, --cores
1
CPU threads (k-mer scan + bootstrap are parallelised). The workload is largely memory-bandwidth-bound, so throughput plateaus well below very high core counts. Bootstrap reproducibility holds only at a fixed--cores (per-thread RNG seeding).
--top-n
all
Plot only the top-N ranked tetramers (cosmetic; does not change the called set).
🚧 Optional analyses — work in progress
These run but are not yet validated in this release; treat output as experimental.
Flag
Default
Meaning
🚧 --event-type RI
—
Intron-retention mode (different region geometry).
🚧 --structure
off
RNA secondary-structure accessibility profiles for enriched motifs (requires ViennaRNA).
🚧 --structure-window
31
Folding window size (bp) for structure profiling.
🚧 --conservation
off
PhyloP conservation profiles (requires pre-downloaded .phylop.bin, see genomes/download_phylop.sh).