{"doi":"10.1101/2023.06.16.543444","title":"CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing","abstract":"Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we developed CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5'capped, full-length transcripts, together with the data processing pipeline LyRic. We benchmarked CapTrap-seq and other popular RNA-seq library preparation protocols in a number of human tissues using both ONT and PacBio sequencing. To assess the accuracy of the transcript models produced, we introduced a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation in RNA spike-in molecules. We found that the vast majority (up to 90%) of transcript models that LyRic derives from CapTrap-seq reads are full-length. This makes it possible to produce highly accurate annotations with minimal human intervention.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":391394,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9538,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":11723,"name":"Julien Lagarde","orcid":"0000-0002-0290-7445","position":1,"is_corresponding":false},{"id":77717,"name":"Hiromi Nishiyori","orcid":null,"position":2,"is_corresponding":false},{"id":874131,"name":"Emilio Palumbo","orcid":"0000-0003-4599-8161","position":3,"is_corresponding":false},{"id":839080,"name":"Carme Arnan","orcid":"0000-0002-7431-2088","position":4,"is_corresponding":false},{"id":11776,"name":"Hazuki Takahashi","orcid":"0000-0001-7315-7349","position":5,"is_corresponding":false},{"id":11487,"name":"Piero Carninci","orcid":"0000-0001-7202-7243","position":6,"is_corresponding":false},{"id":43283,"name":"Barbara Uszczyńska-Ratajczak","orcid":"0000-0003-0150-3841","position":7,"is_corresponding":false},{"id":103609,"name":"Roderic Guigó","orcid":"0000-0002-5738-4477","position":8,"is_corresponding":false},{"id":59135,"name":"Sílvia Carbonell Sala","orcid":"0000-0001-7956-6215","position":0,"is_corresponding":true}],"reference_count":51,"raw_metadata":null,"created_at":"2026-07-19T01:18:47.408273Z","pmid":"37398314","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}