CrossMap: A versatile tool for coordinate conversion between genome assemblies

Research output: Contribution to journalArticle

82 Citations (Scopus)

Abstract

Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc. Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.

Original languageEnglish (US)
Pages (from-to)1006-1007
Number of pages2
JournalBioinformatics
Volume30
Issue number7
DOIs
StatePublished - Apr 1 2014

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Convert
Genome
Sequence Alignment
Genes
Gene transfer
DNA Sequencing
Data visualization
Data Visualization
Data integration
Chromatin Immunoprecipitation
Chromatin
Data Integration
Genomics
RNA
DNA Sequence Analysis
Sequencing
High Throughput
Meta-Analysis
Refinement
DNA

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

CrossMap : A versatile tool for coordinate conversion between genome assemblies. / Zhao, Hao; Sun, Zhifu D; Wang, Jing; Huang, Haojie; Kocher, Jean-Pierre; Wang, Liguo.

In: Bioinformatics, Vol. 30, No. 7, 01.04.2014, p. 1006-1007.

Research output: Contribution to journalArticle

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