Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data

BMC Bioinformatics
Yasunobu Okamura, Kengo Kinoshita

Abstract

Data generated by RNA sequencing (RNA-Seq) is now accumulating in vast amounts in public repositories, especially for human and mouse genomes. Reanalyzing these data has emerged as a promising approach to identify gene modules or pathways. Although meta-analyses of gene expression data are frequently performed using microarray data, meta-analyses using RNA-Seq data are still rare. This lag is partly due to the limitations in reanalyzing RNA-Seq data, which requires extensive computational resources. Moreover, it is nearly impossible to calculate the gene expression levels of all samples in a public repository using currently available methods. Here, we propose a novel method, Matataki, for rapidly estimating gene expression levels from RNA-Seq data. The proposed method uses k-mers that are unique to each gene for the mapping of fragments to genes. Since aligning fragments to reference sequences requires high computational costs, our method could reduce the calculation cost by focusing on k-mers that are unique to each gene and by skipping uninformative regions. Indeed, Matataki outperformed conventional methods with regards to speed while demonstrating sufficient accuracy. The development of Matataki can overcome current limita...Continue Reading

References

Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Nov 20, 2012·Nature Methods·Adam Roberts, Lior Pachter
Dec 4, 2012·Nucleic Acids Research·Takeshi ObayashiKengo Kinoshita
Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
Jun 17, 2014·Bioinformatics·Zhaojun Zhang, Wei Wang
Nov 16, 2014·Nucleic Acids Research·UNKNOWN NCBI Resource Coordinators
Aug 12, 2015·Proceedings of the National Academy of Sciences of the United States of America·Jian ZhangJames L Manley
Apr 5, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter

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Citations

Jun 29, 2021·NAR Genomics and Bioinformatics·Sébastien RiquierThérèse Commes

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Datasets Mentioned

BETA
ERR188125
ERR188362
ERR188171

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Sailfish
GCC
bowtie
simulate
MurMurHash3
KyotoCabinet
RSEM
bzip2
cufflinks
RNA

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