Features & count tables

Running splicekit features creates count tables for junctions, anchors, exons and genes from the project's BAM files.

What are features?

splicekit operates on 4 types of features: junctions, anchors, exons and genes. All feature IDs share the same format: chrstrand_start_stop, e.g. chrX-_154371360_154374505. See Genomic coordinates for how coordinates are reported across splicekit.

Junctions are detected directly from BAM files (independent of any pre-existing gene model), and reported in reference/junctions.tab together with a donor anchor and acceptor anchor — by default the 15nt regions flanking the junction's start and stop. These anchor regions are turned into reference/donor_anchors.gtf / reference/acceptor_anchors.gtf and quantified with featureCounts, alongside exon- and gene-level counts. See File formats for the exact column layouts.

Feature data files

Each individual sample gets one file (table) per feature type, under data/sample_{feature_type}_data/, listing every feature and its count in that sample.

Example: data/sample_exons_data/sample_99.tab

GeneID  Start     End       Length  Symbol  1_test  2_test  3_control  4_control
1       58347029  58347353  325     A1BG    42      31      109        75
1       58347640  58350370  2731    A1BG    0       0       3          1
1       58350651  58351391  741     A1BG    0       0       10         1

Next step: Differential splicing (edgeR), which turns these per-sample count tables into per-comparison differential usage results.