lsec-sicilian-lonp2-pilot-results-v1
Pilot results (5 samples) from re-detecting splice junctions with SICILIAN
(Dehghannasiri, Olivieri, Salzman -- Genome Biology 2021) on raw FASTQ, to test whether the
LONP2 skipped-exon (SE) event's null result (3x via STARsolo -> JAseC/SHIBA) is a methods
artifact. See experiment lsec-sicilian-lonp2 for the full design, red-team review, and
debugging history.
The LONP2 SE event (hg38)
- 5' constitutive exon: chr16:48252131-48252365
- Alternative (skipped) exon: chr16:48256610-48256741
- 3' constitutive exon: chr16:48258618-48258740
- Exclusion junction (skips the alt exon): chr16:48252365-48258618 (SICILIAN exon-boundary
convention) / chr16:48252366-48258617 (STAR SJ.out.tab intron-boundary convention)
Samples
5 samples: fibrosis_1/S38 (SRR28058446) and fibrosis_4/S33 (SRR28058449) -- the only 2 samples
with any current-pipeline read support at the LONP2 SE junction -- plus 3 Healthy controls
(SRR28058450/451/452).
Columns
| Column | Description |
|---|---|
srr_id |
SRA run accession |
sample_label |
Short sample name used throughout this workspace |
group |
F2-3 (fibrosis) or Healthy |
raw_star_exclusion_junction_reads |
Unique-read count for the exclusion junction directly from STAR's SJ.out.tab, BEFORE any UMI deduplication or LSEC-cell restriction -- a cheap, SICILIAN-stats-independent check |
sicilian_exclusion_junction_n_barcodes |
Number of distinct cell barcodes with a SICILIAN-called (GLM-confidence-scored) exclusion-junction event, from sicilian_called_splice_juncs.tsv |
sicilian_exclusion_junction_sum_numreads |
Sum of the numReads field across those barcodes |
lonp2_sj_hits_raw_tsv |
Full raw content of lonp2_sj_hits.tsv (every STAR SJ.out.tab row in the LONP2 genomic window, not just the exclusion junction) |
lonp2_sicilian_hits_full_tsv |
Full raw content of lonp2_sicilian_hits.tsv (every row of sicilian_called_splice_juncs.tsv matching gene name LONP2, i.e. all LONP2 junctions SICILIAN called for this sample, not just the exclusion junction) |
Key finding
The raw STAR SJ.out.tab counts for the exclusion junction show a clean group separation
(F2-3: 45, 42 vs Healthy: 28, 23, 15 -- no overlap). But SICILIAN's own final, cell/UMI-aware,
statistically-scored output (after its GLM confidence model) calls the exclusion junction in
only ONE sample (S38: 2 barcodes, 4 total reads) -- zero in S33 and all 3 Healthy samples. Most
of the raw-read-level signal did not survive SICILIAN's own candidate-junction detection and
statistical filtering. This largely REPRODUCES the original STARsolo->JAseC/SHIBA pipeline's
near-null result rather than revealing a methods-artifact-masked signal, though the single
positive sample is directionally consistent with the original hypothesis (it's an F2-3 sample).
Not included in this dataset (too large, kept on-cluster for reproducibility)
Per-sample class_input.tsv (~14-16GB), GLM_output.txt (~200-450MB), and the fullsicilian_called_splice_juncs.tsv (330MB-3.1GB) remain on turso at/wrk-kappa/users/depinwan/tries/2026-05-05-rerun_Liver_dataset_from_Nature/lsec_sicilian_lonp2/pilot/<SRR>/.