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gene-counter a computational pipeline for the analysis of rna-seq data for gene expression differencesgene-counter计算管道rna-seq数据分析的基因表达差异
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences 1,2. 1,2. 3 3 1¤a Jason S. Cumbie , Jeffrey A. Kimbrel , Yanming Di , Daniel W. Schafer , Larry J. Wilhelm , 1,2 1,4 1 1,2,4¤b Samuel E. Fox , Christopher M. Sullivan , Aron D. Curzon , James C. Carrington , Todd C. Mockler1,2,4¤b, Jeff H. Chang1,2,4* 1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, 2 Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America, 3 Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America, 4 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America Abstract GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)- compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default met
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