Cloud-scale RNA-sequencing differential expression analysis with Myrna
作者： Ben Langmead , Kasper D Hansen , Jeffrey T Leek , None
关键词:
摘要: As sequencing throughput approaches dozens of gigabases per day, there is a growing need for efficient software analysis transcriptome (RNA-Seq) data. Myrna cloud-computing pipeline calculating differential gene expression in large RNA-Seq datasets. We apply to the publicly available data sets and assess goodness fit standard statistical models. from http://bowtie-bio.sf.net/myrna.
biomedcentral.com
springer.com
genomebiology.com
core.ac.uk
elsevier.com
scienceopen.com参考文章(27)
Mark D Robinson, Alicia Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data Genome Biology. ,vol. 11, pp. 1- 9 ,(2010) , 10.1186/GB-2010-11-3-R25
I. Birol, S. D. Jackman, C. B. Nielsen, J. Q. Qian, R. Varhol, G. Stazyk, R. D. Morin, Y. Zhao, M. Hirst, J. E. Schein, D. E. Horsman, J. M. Connors, R. D. Gascoyne, M. A. Marra, S. J. M. Jones, De novo transcriptome assembly with ABySS Bioinformatics. ,vol. 25, pp. 2872- 2877 ,(2009) , 10.1093/BIOINFORMATICS/BTP367
Alicia Oshlack, Matthew J Wakefield, Transcript length bias in RNA-seq data confounds systems biology Biology Direct. ,vol. 4, pp. 14- 14 ,(2009) , 10.1186/1745-6150-4-14
Michael L. Metzker, Sequencing technologies — the next generation Nature Reviews Genetics. ,vol. 11, pp. 31- 46 ,(2010) , 10.1038/NRG2626
, A second generation human haplotype map of over 3.1 million SNPs Nature. ,vol. 449, pp. 851- 861 ,(2007) , 10.1038/NATURE06258
J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, Y. Gilad, RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays Genome Research. ,vol. 18, pp. 1509- 1517 ,(2008) , 10.1101/GR.079558.108
M. C. Schatz, CloudBurst: highly sensitive read mapping with MapReduce Bioinformatics. ,vol. 25, pp. 1363- 1369 ,(2009) , 10.1093/BIOINFORMATICS/BTP236
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology. ,vol. 10, pp. 1- 10 ,(2009) , 10.1186/GB-2009-10-3-R25
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology. ,vol. 28, pp. 511- 515 ,(2010) , 10.1038/NBT.1621
P. Baldi, A. D. Long, A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics. ,vol. 17, pp. 509- 519 ,(2001) , 10.1093/BIOINFORMATICS/17.6.509