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      From RNA-seq reads to differential expression results

      , 1 , 1 , 2 , 1

      Genome Biology

      BioMed Central

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          Abstract

          Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.

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          Most cited references 49

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          Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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            Small-sample estimation of negative binomial dispersion, with applications to SAGE data.

            We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of the negative binomial distribution and compare its performance, in terms of bias, to various other methods. Our estimation scheme outperforms all other methods in very small samples, typical of those from serial analysis of gene expression studies, the motivating data for this study. The impact of dispersion estimation on hypothesis testing is studied. We derive an "exact" test that outperforms the standard approximate asymptotic tests.
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              De novo assembly and analysis of RNA-seq data.

              We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.
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                Author and article information

                Journal
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2010
                22 December 2010
                22 December 2011
                : 11
                : 12
                : 220
                Affiliations
                [1 ]Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
                [2 ]Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
                Article
                gb-2010-11-12-220
                10.1186/gb-2010-11-12-220
                3046478
                21176179
                Copyright ©2010 BioMed Central Ltd
                Categories
                Review

                Genetics

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