RNA-Seq: a revolutionary tool for transcriptomics
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193 citations
193 citations
193 citations
Cites background from "RNA-Seq: a revolutionary tool for t..."
...…on high-throughput sequencing and RNA-seq 1 Principles of high throughput sequencing technology: (Metzker 2010) 2 Principles of RNA-seq: (Wang et al. 2009; Oshlack et al. 2010; Ozsolak & Milos 2011) 3 Principles of transcriptome assembly (Martin & Wang 2011) with particular reference to…...
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...Box 1 Quick links to useful entry points to the field Overview on high-throughput sequencing and RNA-seq 1 Principles of high throughput sequencing technology: (Metzker 2010) 2 Principles of RNA-seq: (Wang et al. 2009; Oshlack et al. 2010; Ozsolak & Milos 2011) 3 Principles of transcriptome assembly (Martin & Wang 2011) with particular reference to plants (Jain 2012) Applications in ecology and evolutionary biology 1 General next-generation sequencing applications including RNA-seq: (Ekblom & Galindo 2011) 2 Special issues on next-generation sequencing including RNA-seq: (Stapley et al. 2010; Tautz et al. 2010; Orsini et al. 2013) Practical guidance and examples for useful tools 1 Review on computational methods and tools: (Pepke et al. 2009; Magi et al. 2010; Bao et al. 2011; Garber et al. 2011; Lee et al. 2012) 2 Guidance in the design and analysis of RNA-seq experiments: (De Wit et al. 2012; Vijay et al. 2013) 3 Statistical consideration for RNA-seq data: (Bullard et al. 2010; Kvam et al. 2012) 4 Preprocessing and quality control tools: NGSQCtoolkit (Patel & Jain 2012), fastQCtoolkit (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/), 5 Mapping tools: (Trapnell & Salzberg 2009; Bao et al. 2011) 6 Gene name assignment: e.g. BLAST2GO, SATSUMA, SPINES (for details and references see Vijay et al. 2013) 7 Data visualization tools: e.g. MapView (Bao et al. 2009), IGV (Thorvaldsd ottir et al. 2013), Tablet (Milne et al. 2010) 8 Utility suites saving own effort: BEDtools (Quinlan & Hall 2010), SAMtools (Li et al. 2009) 9 Variant calling and genotyping: review (Nielsen et al. 2011), GATK (DePristo et al. 2011), freebayes (http://bioinfor- matics.bc.edu/marthlab/FreeBayes); 10 Gene function: Gene ontology (Gene Ontology Consortium 2004), gene ontology tools http://neurolex.org/wiki/Cat- egory:Resource:Gene_Ontology_Tools 11 Gene interaction pathways: e.g. KeGG pathway (Ogata et al. 1999; http://www.genome.jp/kegg/pathway.html), STRING database (Szklarczyk et al. 2011; http://string-db.org/) (http://string-db.org/) 12 Galaxy: a useful online platform to analyse RNA-seq data: (Goecks et al. 2010) 13 The Bioconductor package: (Gentleman et al. 2004) www.bioconductor.org 14 Differential expression software: e.g. DESeq (Anders & Huber 2010), edgeR (Robinson et al. 2010), baySeq (Hardcastle & Kelly 2010), NOIseq (Tarazona et al. 2011) 15 Alternative splicing software: e.g. Cufflinks (Trapnell et al. 2012), DEXSeq (Anders et al. 2012), EBSeq (Leng N et al. 2013), MISO (Katz et al. 2010) Where to find help?...
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...RNA-seq: High-throughput shotgun transcriptome sequencing....
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...1 Principles of high throughput sequencing technology: (Metzker 2010) 2 Principles of RNA-seq: (Wang et al. 2009; Oshlack et al. 2010; Ozsolak & Milos 2011) 3 Principles of transcriptome assembly (Martin & Wang 2011) with particular reference to plants (Jain 2012)...
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192 citations
Cites background or methods from "RNA-Seq: a revolutionary tool for t..."
...preferred methodology for the study of gene expression [3, 5]....
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...COUNT BIASAND NORMALIZATION After the first optimistic expectation of a relative ease of analysis of RNA-seq data [3], many works have highlighted the need for a careful normalization of count data before assessing differential gene expression [9, 52–56] to correct for different sources of bias....
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...Moreover, reverse-transcription can either over- or under-represent 30 end of transcripts if performed with poly-dT oligomers or random hexamers, respectively [1, 3, 19]....
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...high throughput and relatively low costs [3]....
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192 citations
Cites background from "RNA-Seq: a revolutionary tool for t..."
...Compared to other technologies such as microarrays, RNA-seq technology offers the following benefits (Ozsolak and Milos, 2011; Wang et al., 2009)....
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References
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"RNA-Seq: a revolutionary tool for t..." refers methods in this paper
...There are several programs for mapping reads to the genome, including ELAND, SOA...
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