Output & Interpretation

Results land in results/<name>/<timestamp>_<genome>_w<hw>_..._ew<ew>_..._b<boot>_.../.

Key files

File	What it is
`-tets-.pdf`	The RNA splicing map — per-position motif-cluster frequency, enhanced (red) vs silenced (blue) vs control, for the enriched tetramers. The headline result.
`enriched_tetramers.txt`	Plain list of tetramers that passed both significance filters.
`-tets-.csv`	Per-tetramer enrichment table (region-wise Fisher and empirical p-values).
`All_group_{enh,sil,both}-*.csv`	Per-position occupancy curves for all candidate tetramers, split by group (feed the splicing map and the MaRs cosine-similarity step).
`Enh_`, `Sil_`, `ES_`, `e-`, `s-*`	Group-specific enrichment matrices (enhanced-only, silenced-only, both).
`regions.csv`	The R1/R2/R3 region classification per tetramer.
`cluster_ids.txt`	Cluster assignments for the enriched motifs.
`bootstrap_<b>.tsv` / `.Rdata`	The empirical-FDR null draws (reused on resume — do not delete if re-scoring).
`no_enriched.txt`	Written instead of plots when nothing passes the filters (usually too few exons or thresholds too strict).
`rnamotifs.log`	Full run log.

Reading the RNA splicing map

The map plots, for each enriched motif, the fraction of exons carrying a motif cluster at each position around the splice sites, as three curves: enhanced, silenced, control.

A peak of the enhanced (or silenced) curve that rises above the control curve at a given region marks where that motif's clusters concentrate to drive regulation.
Position matters: e.g. pyrimidine motifs peaking in the upstream intron near silenced exons is the classic RNAmotifs readout of intronic silencing.
The region labels R1 / R2 / R3 correspond to upstream intron / exon body / downstream intron (skipped exon).

A motif is reported only if it beats both --p-fisher (Fisher's exact, regulated vs control) and --p-empirical (bootstrap null). Loosen these (and/or --min-height) if you expect signal but see no_enriched.txt.

Extracting motif coordinates

./rnamotifs-extract results/MYRBP/<run>             # all enriched, TSV
./rnamotifs-extract results/MYRBP/<run> -t YCAY --bed
./rnamotifs-extract results/MYRBP/<run> -c silenced -o sil_motifs.tsv

Option	Description	Default
`results_dir`	Path to a completed results folder (positional)	required
`-t, --tetramer`	Extract for a specific tetramer	all enriched
`-c, --category`	`enhanced`, `silenced`, or `both`	both
`-o, --output`	Output file	stdout
`--bed`	Output in BED format	TSV

← Back to tutorial index

← Back to tutorial overview