Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Koen Van den Berge; Hsin-Jung Chou; Hector Roux de Bézieux; Kelly Street; Davide Risso; John Ngai; Sandrine Dudoit

doi:10.1101/2021.01.26.428252

New Results

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

View ORCID ProfileKoen Van den Berge, Hsin-Jung Chou, View ORCID ProfileHector Roux de Bézieux, View ORCID ProfileKelly Street, View ORCID ProfileDavide Risso, View ORCID ProfileJohn Ngai, View ORCID ProfileSandrine Dudoit

doi: https://doi.org/10.1101/2021.01.26.428252

Koen Van den Berge

1Department of Statistics, University of California, Berkeley, CA, USA

2Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

3Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for Koen Van den Berge

Hsin-Jung Chou

4Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Hector Roux de Bézieux

5Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA

6Center for Computational Biology, University of California, Berkeley, CA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for Hector Roux de Bézieux

Kelly Street

7Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA

8Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for Kelly Street

Davide Risso

9Department of Statistical Sciences, University of Padova, Italy

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for Davide Risso

John Ngai

4Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

10Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for John Ngai

Sandrine Dudoit

1Department of Statistics, University of California, Berkeley, CA, USA

5Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA

6Center for Computational Biology, University of California, Berkeley, CA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
ORCID record for Sandrine Dudoit
For correspondence: sandrine@stat.berkeley.edu

Abstract
Full Text
Info/History
Metrics
Supplementary material
Preview PDF

Supplementary Material[supplements/428252_file02.pdf]

View the discussion thread.

PreviousNext

Posted May 20, 2021.

Download PDF

Supplementary Material

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Your Email *

Your Name *

Send To *

Enter multiple addresses on separate lines or separate them with commas.

You are going to email the following Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Message Subject (Your Name) has forwarded a page to you from bioRxiv

Message Body (Your Name) thought you would like to see this page from the bioRxiv website.

Your Personal Message

CAPTCHA

This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai, Sandrine Dudoit

bioRxiv 2021.01.26.428252; doi: https://doi.org/10.1101/2021.01.26.428252

Share This Article:

Citation Tools

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai, Sandrine Dudoit

bioRxiv 2021.01.26.428252; doi: https://doi.org/10.1101/2021.01.26.428252

Citation Manager Formats

BibTeX
Bookends
EasyBib
EndNote (tagged)
EndNote 8 (xml)
Medlars
Mendeley
Papers
RefWorks Tagged
Ref Manager
RIS
Zotero

Tweet Widget
Facebook Like
Google Plus One

Subject Area

Bioinformatics

Subject Areas

All Articles

Animal Behavior and Cognition (4680)
Biochemistry (10353)
Bioengineering (7670)
Bioinformatics (26325)
Biophysics (13521)
Cancer Biology (10682)
Cell Biology (15430)
Clinical Trials (138)
Developmental Biology (8496)
Ecology (12818)
Epidemiology (2067)
Evolutionary Biology (16848)
Genetics (11393)
Genomics (15476)
Immunology (10610)
Microbiology (25204)
Molecular Biology (10220)
Neuroscience (54447)
Paleontology (401)
Pathology (1668)
Pharmacology and Toxicology (2897)
Physiology (4341)
Plant Biology (9243)
Scientific Communication and Education (1586)
Synthetic Biology (2557)
Systems Biology (6778)
Zoology (1465)