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Transcript Assembly

Definition
AI-generated

Transcript assembly (or transcript reconstruction) is the computational inference of gene structures and isoforms from RNA sequencing reads—typically by spliced alignment to a genome followed by graph-based or optimization methods that chain exons into transcripts.

Topics
Sequencing and omics tech
Related
Alternative Splicing Genome Annotation Long-Read RNA-seq

Why it matters in GWAS

eQTL and TWAS analyses assume a transcriptome reference; assemblies from the same tissue or cell type as the QTL panel can reveal unannotated isoforms or improve quantification. Disagreement between catalog annotation (GENCODE) and study-specific assembly affects which junctions and isoforms are tested.

Example usage

"Functional interpretation integrated Transcript Assembly evidence with GWAS signals in relevant cell states."

Alternative Splicing Genome Annotation Long-Read RNA-seq RNA Sequencing (RNA-seq) StringTie Transcriptome-Wide Association Study (TWAS)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Pertea M, et al. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
← Transcript Transcript quantification →

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