quartet_s84_c_gencode_v43_filter_filter_sqanti.cds.gtf

Quartet-specific transcriptome assembly using a hybrid long- and short-read approach. Seven batches of high-quality lrRNA-seq libraries (SNR ≥ 10) and one batch of matched Illumina SR libraries were assembled with StringTie3 (v3.0.0) in hybrid mode (--mix), which concatenates the long- and short-read BAMs for each sample. Mono-exonic (unspliced) contigs were excluded. Each sample’s isoform assembly was then merged using StringTie3 –merge, and each isoform was re-quantified for each sample with StringTie3 –estimate against GENCODE v43. Isoforms were compared with the GENCODE v43 reference annotation to determine novelty. All annotated isoforms were then kept first, while novel isoforms were kept only if they were expressed in ≥ 3 samples within a batch. The combined set was refined using SQANTI3 (v5.2.0)with default quality-control filters and the same GENCODE annotation. Finally, any isoform failing SQANTI3 flags or falling below the re-quantified expression threshold was discarded, yielding the Quartet hybrid reference transcriptome.