Differential splicing (edgeR)¶

Running edgeR analysis on features (junctions, anchors, exons, genes) is a single command:

splicekit edgeR              # all feature types
splicekit edgeR junctions    # a single feature type
splicekit edgeR exons
splicekit edgeR anchors
splicekit edgeR genes

Donor/acceptor anchor results are then merged back into the corresponding junction results by splicekit juan (part of splicekit process), so a junction's row also carries its anchors' edgeR statistics.

Results files¶

Results are stored in results/results_edgeR_{feature_type}.tab, where feature_type is one of genes, exons, junctions, donor_anchors, acceptor_anchors. Only results with FDR < splicekit.config.edgeR_FDR_thr are reported (sorted by FDR), each linked to JBrowse2 via a URL.

To explore all results without the FDR filter, use results/results_edgeR_{feature_type}_all.tab.

General columns¶

Column	Example	Description
`result_id`	`r1`	Integer result identifier, starting at 1.
`comparison`	`test_control`	Comparison name, from `annotation/comparisons.tab`.
`compound`	`treatment1`	Name of the treatment/compound tested.
`feature_id`	`chr1+_17741_17839`	ID of the reported feature: a gene/exon/junction/`[donor,acceptor]_anchor` ID.
`chr`	`1`	Chromosome of the feature.
`strand`	`+`	Strand of the feature (`+` or `-`).
`feature_start`	`17741`	Start of the feature (numerically, start < stop). See Genomic coordinates.
`feature_stop`	`17839`	Stop of the feature (numerically, stop > start).
`feature_length`	`250`	`feature_stop - feature_start + 1`.
`gene_id`	`ENSG00000120948`	Ensembl or RefSeq gene ID.
`gene_name`	`TARDBP`	Corresponding to `gene_id`.
`sum_feature_test`	`1000`	Sum of counts for this feature across all test samples.
`sum_feature_control`	`1000`	Sum of counts for this feature across all control samples.
`jbrowse_loc`	`3:342321..351243`	Genomic region shown in the JBrowse view.
`jbrowse_url`		Link to the JBrowse view.
`logFC`		Log fold change, from edgeR.
`exon.F`		`exon.F` statistic, from edgeR.
`p_value`		p-value, from edgeR.
`fdr`		False discovery rate, from edgeR.

Junction-specific (additional) columns¶

Column	Example	Description
`annotated`	`AA`	Two-letter code `AA`/`AN`/`NA`/`NN`: first letter for the donor site (5' of junction), second for the acceptor site (3' of junction); `A` = touches an annotated exon, `N` = does not.
`donor_anchor_id`		ID of the donor anchor linked to this junction.
`acceptor_anchor_id`		ID of the acceptor anchor linked to this junction.
`UTR`		`first_exon_{start_pos}` if the junction touches any transcript's first exon of the gene.

Exon-specific (additional) columns¶

Column	Example	Description
`delta_PSI`		`test_PSI - control_PSI` (percentage spliced-in).

Next: Motif & RNA-binding analysis runs on the sequences around the regulated features found here.