GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

摘要: GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, applicable prokaryotes and non-model organisms without an available genome reference sequence. For alignments, configured CASHX, Bowtie, BWA, but end user can any Sequence Alignment/Map (SAM)-compliant program preference. To analyze expression, be run with one three statistics packages that are based on variations the negative binomial distribution. The default method new simple statistical test we developed over-parameterized version also includes different methods assessing differentially expressed features enriched ontology (GO) terms. Results transparent systematically stored MySQL relational database facilitate additional analyses as well quality assessment. We used next generation sequencing generate small-scale RNA-Seq dataset derived from heavily studied defense response Arabidopsis thaliana process data. Collectively, support analysis microarrays observed substantial overlap results each demonstrates suited handling unique characteristics small sample sizes high variability counts.