{"doi":"10.1101/2020.04.07.029967","title":"Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data","abstract":"Abstract Motivation Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcriptlevel abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects. Results We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly-reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result. Availability Terminus is implemented in Rust, and is freely-available and open-source. It can be obtained from https://github.com/COMBINE-lab/Terminus . Contact rob@cs.umd.edu Supplementary information Supplementary data are available at Bioinformatics online.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":123594,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9463,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":52013,"name":"Avi Srivastava","orcid":"0000-0001-9798-2079","position":1,"is_corresponding":false},{"id":18144,"name":"Héctor Corrada Bravo","orcid":"0000-0002-1255-4444","position":2,"is_corresponding":false},{"id":29945,"name":"Michael I. Love","orcid":"0000-0001-8401-0545","position":3,"is_corresponding":false},{"id":87821,"name":"Rob Patro","orcid":"0000-0001-8463-1675","position":4,"is_corresponding":false},{"id":497433,"name":"Hirak Sarkar","orcid":"0000-0003-3636-7384","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-07-18T23:15:03.403566Z","pmid":null,"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":[]}