Table 2:
Transcript Classifications and Definitions used by the LRGASP computational evaluation.
| Classification | Description |
|---|---|
| Full Splice Match (FSM) | Transcripts matching a reference transcript at all splice junctions |
| Incomplete Splice Match (ISM) | Transcripts matching consecutive, but not all, splice junctions of the reference transcripts |
| Novel in Catalog (NIC) | Transcripts containing new combinations of 1) already annotated splice junctions, 2) novel splice junctions formed from already annotated donors and acceptors, or 3) unannotated intron retention |
| Novel Not in Catalog (NNC) | Transcripts using novel donors and/or acceptors |
| Reference Match (RM) | FSM transcript with 5´ and 3énds within 50 nts of the transcription start site (TSS)/transcription termination site (TTS) annotation |
| 3´ poly(A) supported | Transcript with poly(A) signal sequence support or short-read 3’ end sequencing (e.g. QuantSeq) support at the 3énd |
| 5´ CAGE supported | Transcript with CAGE support at the 5énd |
| 3´ reference supported | Transcript with 3énd within 50 nts from a reference transcript TTS |
| 5´ reference supported | Transcript with 5énd within 50 nts from a reference transcript TSS |
| Supported Reference Transcript Model (SRTM) | FSM/ISM transcript with 5´ end within 50 nts of the TSS or has CAGE support AND 3´ end within 50 nts of the TTS or has poly(A) signal sequence support or short-read 3’ end sequencing support |
| Supported Novel Transcript Model (SNTM) | NIC/NNC transcript with 5´ end within 50 nts of the TSS or CAGE support AND 3´ end within 50 nts of the TTS or has poly(A) signal sequence support or short-read 3’ end sequencing support AND Illumina read support at novel junctions |
| % Long Read Coverage (%LRC) | Fraction of the transcript model sequence length mapped by one or more long reads |
| Read multiplicity | Number of assigned transcripts per read |
| Redundancy | # LR transcript models / reference model |
| Longest Junction | |
| Chain ISM | # junctions in ISM / # junctions reference |
| NIC / NNC | # reference junctions / # junctions in NIC/NNC |
| Intron retention (IR) level | Number of IR within the NIC category |
| Illumina Splice Junction (SJ) Support | % SJ in transcript model with Illumina support |
| Full Illumina Splice Junction Support | % transcripts in category with all SJ supported |
| % Novel Junctions | # of new junctions / total # junctions |
| % Non-canonical junctions | # of non-canonical junctions / total # junctions |
| % Non-canonical transcripts | % transcripts with at least one non-canonical junction |
| Intra-priming | Evidence of intra-priming (described in 15) |
| RT-switching | Evidence of RT-switching (described in 15) |