Hello all,
I am wondering how I should interpret the “smaller_splice” in the image / table below.
Some context: this is a gene on the negative strand, so I would understand that the junction_Start is the 3′ splice acceptor site and junction_End 5′ splice donor site.
The “big_splice” seems to make sense to me, starting at the end of exon1 going to the cassette exon, but the “smaller_splice” seems to start in the middle of the intron, does this mean that alphagenome predicts that anything before is an exon, or could it be that it is a second splice donor that is ignored after the one that should be there at the end of exon1?
Thank you in advance for the feedback.
| junction_Start | junction_End | name | output_type | variant_scorer | track_name | track_strand | Assay title | ontology_curie | biosample_name | biosample_type | raw_score | quantile_score |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 173915186 | 173917218 | big_splice | SPLICE_JUNCTIONS | SpliceJunctionScorer() | junction_UBERON:0002107 polyA plus RNA-seq | . | polyA plus RNA-seq | UBERON:0002107 | liver | tissue | 0.20898438 | 0.993351 |
| 173915186 | 173917218 | big_splice | SPLICE_JUNCTIONS | SpliceJunctionScorer() | junction_UBERON:0002107 total RNA-seq | . | total RNA-seq | UBERON:0002107 | liver | tissue | 0.1607666 | 0.9912486 |
| 173915115 | 173916406 | smaller_splice | SPLICE_JUNCTIONS | SpliceJunctionScorer() | junction_UBERON:0002107 total RNA-seq | . | total RNA-seq | UBERON:0002107 | liver | tissue | 0.12902832 | 0.9890026 |
| 173915115 | 173916406 | smaller_splice | SPLICE_JUNCTIONS | SpliceJunctionScorer() | junction_UBERON:0002107 polyA plus RNA-seq | . | polyA plus RNA-seq | UBERON:0002107 | liver | tissue | 0.11065674 | 0.9868027 |