Genome build information is an essential part of genomic track files

Chakravarthi Kanduri; Diana Domanska; Eivind Hovig; Geir Kjetil Sandve

doi:10.1186/s13059-017-1312-1

Genome build information is an essential part of genomic track files

Genome Biol. 2017 Sep 14;18(1):175. doi: 10.1186/s13059-017-1312-1.

Authors

Chakravarthi Kanduri^{1

2}, Diana Domanska¹, Eivind Hovig^{1

3

4}, Geir Kjetil Sandve^{5

6}

Affiliations

¹ Department of Informatics, University of Oslo, 0316, Oslo, Norway.
² K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0318, Oslo, Norway.
³ Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424, Oslo, Norway.
⁴ Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424, Oslo, Norway.
⁵ Department of Informatics, University of Oslo, 0316, Oslo, Norway. geirksa@ifi.uio.no.
⁶ K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0318, Oslo, Norway. geirksa@ifi.uio.no.

Abstract

Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Although not a substitute for best practices, we also provide a tool to predict the genome build version of genomic track files.

Publication types

Letter
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Databases, Genetic
Datasets as Topic
Genome*
Genome, Human
Genomics*
Humans