{"doi":"10.1101/2024.05.20.595042","title":"CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data","abstract":"Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":490989,"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":0.9543,"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":1336745,"name":"Budhaditya Chatterjee","orcid":null,"position":1,"is_corresponding":false},{"id":446542,"name":"Yuko Ohta","orcid":null,"position":2,"is_corresponding":false},{"id":1336746,"name":"Katrina Gorga","orcid":null,"position":3,"is_corresponding":false},{"id":1336747,"name":"Carly Blair","orcid":null,"position":4,"is_corresponding":false},{"id":737207,"name":"Elizabeth Hill","orcid":"0000-0002-3412-8278","position":5,"is_corresponding":false},{"id":1336417,"name":"Zachary Fasana","orcid":"0009-0004-5915-8491","position":6,"is_corresponding":false},{"id":1336418,"name":"Adedola Adebamowo","orcid":"0009-0003-3931-8219","position":7,"is_corresponding":false},{"id":1336748,"name":"Farah Ammar","orcid":null,"position":8,"is_corresponding":false},{"id":689133,"name":"Ivan Košík","orcid":"0000-0001-5756-5182","position":9,"is_corresponding":false},{"id":780511,"name":"Vel Murugan","orcid":"0000-0002-7368-7742","position":10,"is_corresponding":false},{"id":415859,"name":"Wilbur H. Chen","orcid":"0000-0001-7741-5536","position":11,"is_corresponding":false},{"id":513298,"name":"Nevil J. Singh","orcid":"0000-0002-8384-9290","position":12,"is_corresponding":false},{"id":234800,"name":"Martin Meier‐Schellersheim","orcid":"0000-0002-8754-6377","position":13,"is_corresponding":false},{"id":563083,"name":"Christopher T. Boughter","orcid":"0000-0002-7106-4699","position":0,"is_corresponding":true}],"reference_count":17,"raw_metadata":null,"created_at":"2026-07-19T02:08:41.211111Z","pmid":"38903111","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":[]}