{"doi":"10.1093/bioinformatics/btaa923","title":"HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data","abstract":"Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline Hi-C-based TE analyzer (HiTea) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole-genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE-insertion landscape. We employ the pipeline to identify TE-insertions from human cell-line Hi-C samples. AVAILABILITY AND IMPLEMENTATION: HiTea is available at https://github.com/parklab/HiTea and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2020,"id":110676,"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":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8774,"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":279168,"name":"Chong Chu","orcid":"0000-0002-0796-2339","position":1,"is_corresponding":false},{"id":23417,"name":"B. Alver","orcid":"0000-0002-5019-7652","position":2,"is_corresponding":false},{"id":23358,"name":"Soohyun Lee","orcid":"0000-0002-3594-6213","position":3,"is_corresponding":false},{"id":13712,"name":"Eunjung Alice Lee","orcid":"0000-0002-6574-9261","position":4,"is_corresponding":false},{"id":1821,"name":"Peter J. Park","orcid":"0000-0001-9378-960X","position":5,"is_corresponding":false},{"id":108497,"name":"Dhawal Jain","orcid":"0000-0001-9437-7201","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-18T23:13:01.914939Z","pmid":"33136153","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":[]}