Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genome build information is an essential part of genomic track files

View ORCID ProfileChakravarthi Kanduri, Diana Domanska, Eivind Hovig, View ORCID ProfileGeir Kjetil Sandve
doi: https://doi.org/10.1101/120923
Chakravarthi Kanduri
1Department of Informatics, University of Oslo, Oslo, Norway
2K. G. Jebsen Coeliac Disease Research Centre
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chakravarthi Kanduri
Diana Domanska
1Department of Informatics, University of Oslo, Oslo, Norway
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eivind Hovig
3Department of Tumor Biology, Institute for Cancer Research
4Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital
1Department of Informatics, University of Oslo, Oslo, Norway
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Geir Kjetil Sandve
1Department of Informatics, University of Oslo, Oslo, Norway
2K. G. Jebsen Coeliac Disease Research Centre
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Geir Kjetil Sandve
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. It is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Here, we demonstrate that this crucial metadatum (or rather datum) is often isolated from the genomic track files in public repositories and journal articles, which could be a major time thief. We propose best practices to ensure that genome build version is always carried along with genomic track files. Although not a substitute to the best practices, we also provide a tool to predict the genome build version of genomic track files.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted March 27, 2017.
Download PDF

Supplementary Material

Email

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.

Enter multiple addresses on separate lines or separate them with commas.
Genome build information is an essential part of genomic track files
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genome build information is an essential part of genomic track files
Chakravarthi Kanduri, Diana Domanska, Eivind Hovig, Geir Kjetil Sandve
bioRxiv 120923; doi: https://doi.org/10.1101/120923
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Genome build information is an essential part of genomic track files
Chakravarthi Kanduri, Diana Domanska, Eivind Hovig, Geir Kjetil Sandve
bioRxiv 120923; doi: https://doi.org/10.1101/120923

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 (3689)
  • Biochemistry (7796)
  • Bioengineering (5675)
  • Bioinformatics (21284)
  • Biophysics (10578)
  • Cancer Biology (8174)
  • Cell Biology (11945)
  • Clinical Trials (138)
  • Developmental Biology (6763)
  • Ecology (10401)
  • Epidemiology (2065)
  • Evolutionary Biology (13866)
  • Genetics (9708)
  • Genomics (13073)
  • Immunology (8146)
  • Microbiology (20014)
  • Molecular Biology (7853)
  • Neuroscience (43057)
  • Paleontology (319)
  • Pathology (1279)
  • Pharmacology and Toxicology (2258)
  • Physiology (3351)
  • Plant Biology (7232)
  • Scientific Communication and Education (1312)
  • Synthetic Biology (2006)
  • Systems Biology (5538)
  • Zoology (1128)