File formats¶
reference/junctions.tab¶
Contains all junctions detected across every sample in the project. Only junctions that could be annotated to a gene are reported — including "novel" junctions that don't touch a RefSeq/Ensembl-annotated exon, as long as the junction's start and stop fall inside an annotated gene (see the annotated column).
| Column | Example | Description |
|---|---|---|
junction_id |
chr1+_17741_17839 |
Unique ID: chrstrand_start_stop. |
donor_anchor_id |
chr1+_17725_17740 |
Matching donor anchor ID — by default the 15nt region upstream of the junction start. |
acceptor_anchor_id |
chr1+_17840_17855 |
Matching acceptor anchor ID — by default the 15nt region downstream of the junction stop. |
gene_id |
ENSG00000120948 |
Ensembl or RefSeq gene ID. A junction can be non-annotated (annotated != "AA") but still assigned to a gene, meaning its start/stop fall inside the gene. |
gene_name |
TARDBP |
Corresponding to gene_id. |
chr |
1 |
Chromosome. |
strand |
+ |
+ or -. |
annotated |
AA |
Two-letter code AA/AN/NA/NN — see Genomic coordinates and edgeR results. |
count |
553 |
Raw read count across all samples in the project supporting this junction. |
reference/donor_anchors.gtf and reference/acceptor_anchors.gtf¶
GTF files generated from all donor/acceptor anchors in reference/junctions.tab. Used by featureCounts to build anchor count tables across the project's samples.
results/results_edgeR_{feature_type}.tab¶
See Differential splicing (edgeR): Results files for the full column reference (general columns, plus junction- and exon-specific additions).
data/sample_{feature_type}_data/*.tab¶
See Features & count tables: Feature data files.