{"doi":"10.1093/bib/bbae251","title":"RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data","abstract":"Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.","journal":"Briefings in Bioinformatics","year":2024,"id":480235,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9599,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1319513,"name":"Xinrui Shi","orcid":"0009-0001-2188-3696","position":1,"is_corresponding":false},{"id":527543,"name":"Samuel Haddox","orcid":null,"position":2,"is_corresponding":false},{"id":1180441,"name":"Justin Elfman","orcid":"0000-0003-0516-5325","position":3,"is_corresponding":false},{"id":1319847,"name":"Syed Basil Ahmad","orcid":null,"position":4,"is_corresponding":false},{"id":1002712,"name":"Sarah Lynch","orcid":null,"position":5,"is_corresponding":false},{"id":1319848,"name":"Tommy Manley","orcid":null,"position":6,"is_corresponding":false},{"id":1319849,"name":"Claire Piczak","orcid":null,"position":7,"is_corresponding":false},{"id":1319514,"name":"Christopher Phung","orcid":"0009-0005-2993-7037","position":8,"is_corresponding":false},{"id":1192252,"name":"Yunan Sun","orcid":null,"position":9,"is_corresponding":false},{"id":1319850,"name":"Aadi Sharma","orcid":null,"position":10,"is_corresponding":false},{"id":15834,"name":"Hui Li","orcid":"0000-0002-7879-1792","position":11,"is_corresponding":false},{"id":464105,"name":"Sandeep Singh","orcid":"0000-0001-5361-4303","position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-07-19T02:06:58.305365Z","pmid":"38796690","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":[]}