zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

GigaScience
Swati ParekhInes Hellmann

Abstract

Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolut...Continue Reading

References

Nov 22, 2011·Nature Methods·Teemu KiviojaJussi Taipale
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 24, 2013·Nature Methods·Saiful IslamSten Linnarsson
Jan 21, 2014·Molecular Cell·Gert-Jan HendriksHelge Großhans
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Apr 22, 2014·Nature Methods·Dominic GrünAlexander van Oudenaarden
Apr 14, 2015·Nature Biotechnology·Rahul SatijaAviv Regev
Nov 7, 2015·Cell·Dominic Grün, Alexander van Oudenaarden
Jan 5, 2016·Nature Neuroscience·Bosiljka TasicHongkui Zeng
Apr 29, 2016·Genome Biology·Tamar HashimshonyItai Yanai
May 10, 2016·Scientific Reports·Swati ParekhInes Hellmann
Nov 9, 2016·Nature Biotechnology·Allon WagnerNir Yosef
Dec 9, 2016·Nature Protocols·Rapolas ZilionisLinas Mazutis
Jan 17, 2017·Nature Communications·Grace X Y ZhengJason H Bielas
Feb 19, 2017·Molecular Cell·Christoph ZiegenhainWolfgang Enard
Mar 7, 2017·Nature Methods·Valentine SvenssonSarah A Teichmann
May 16, 2017·Nature Methods·Catalina A VallejosJohn C Marioni
Aug 29, 2017·Nature Methods·Naomi HabibAviv Regev
Oct 17, 2017·Bioinformatics·Beate ViethInes Hellmann
Nov 29, 2017·Scientific Reports·Hannah HochgernerSten Linnarsson
Dec 6, 2017·ELife·Aviv RegevUNKNOWN Human Cell Atlas Meeting Participants
Feb 24, 2018·Cell·Xiaoping HanGuoji Guo
Feb 27, 2018·Nature Methods·Charlotte Soneson, Mark D Robinson
Mar 27, 2018·Briefings in Functional Genomics·Christoph ZiegenhainWolfgang Enard
May 31, 2018·GigaScience·Swati ParekhInes Hellmann

❮ Previous
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Citations

Jun 26, 2018·PLoS Computational Biology·Luke ZappiaAlicia Oshlack
Aug 11, 2018·PLoS Computational Biology·Luyi TianMatthew E Ritchie
Jun 30, 2019·Transplant International : Official Journal of the European Society for Organ Transplantation·Anastasia MinervinaIlgar Mamedov
Dec 17, 2019·Science Advances·Micha Sam Brickman RaredonLaura E Niklason
Jan 29, 2020·The Journal of Clinical Investigation·Takashi MaeharaShiv Pillai
Jul 7, 2019·Scientific Reports·Shuaijun WangStefan Zahler
Jul 21, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Natalia JuizNelson Dusetti
May 3, 2019·BMC Bioinformatics·Zhe WangJoshua D Campbell
Jun 21, 2020·Nature Protocols·Bram Van de SandeStein Aerts
Sep 27, 2018·Nature Protocols·Michael Hagemann-JensenOmid R Faridani
Jun 21, 2019·Molecular Systems Biology·Malte D Luecken, Fabian J Theis
Oct 13, 2019·Nature Communications·Beate ViethInes Hellmann
Jun 3, 2020·Nature Reviews. Gastroenterology & Hepatology·Prakash RamachandranNeil C Henderson
Jun 24, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yuhei KiritaBenjamin D Humphreys
May 31, 2018·GigaScience·Swati ParekhInes Hellmann
Jul 28, 2018·Nature Communications·Johannes W BagnoliWolfgang Enard
Dec 26, 2018·BMC Genomics·Dario RomagnoliMatteo Benelli
Jun 11, 2020·Nature Biotechnology·Michael Hagemann-JensenRickard Sandberg
Apr 24, 2020·Nature Communications·Keren Bahar HalpernShalev Itzkovitz
Jun 13, 2020·Nature Communications·Anna KlimovskaiaMaximilian Nickel
Mar 27, 2019·Therapeutic Advances in Ophthalmology·Nicholas Owen, Mariya Moosajee
Sep 20, 2019·Nature Metabolism·Shani Ben-MosheShalev Itzkovitz
Apr 29, 2020·Nature Biotechnology·Jiarui DingJoshua Z Levin
Jun 26, 2020·Frontiers in Cell and Developmental Biology·Yutian LeiHans-Joachim Anders
Nov 26, 2020·Nature Communications·Christopher B MulhollandHeinrich Leonhardt
Aug 18, 2020·American Journal of Respiratory Cell and Molecular Biology·Jeffrey R KoenitzerBenjamin D Humphreys
Dec 3, 2020·Nucleic Acids Research·Oliver HahnTony Wyss-Coray
Dec 18, 2020·Molecular Systems Biology·Hassan MassalhaShalev Itzkovitz
Jun 3, 2020·The Journal of Allergy and Clinical Immunology·Cory A PeruginoShiv Pillai
Jan 12, 2021·PLoS Computational Biology·Charlotte SonesonMichael B Stadler
Jan 15, 2021·Arteriosclerosis, Thrombosis, and Vascular Biology·Jean AcostaPeter van Galen
Sep 11, 2020·Experimental Eye Research·Andrew P VoigtTodd E Scheetz
Dec 6, 2020·Neuron·Chuchu ZhangStephen D Liberles
Dec 31, 2020·Developmental Cell·Gianluca AmadeiMagdalena Zernicka-Goetz
Feb 4, 2021·Scientific Data·Xin ChenCharles Wang
Feb 12, 2021·Scientific Reports·Johanna GeuderWolfgang Enard

❮ Previous
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