RNA-Seq Analysis Tools from the Broad Institute from RNA-Seq Blog

RNA-Seq Analysis Tools from the Broad Institute

from RNA-Seq Blog by admin

GenePattern offers a suite of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, and differential expression. The modules have been adapted from widely-used tools. GenePattern also provides pipelines that allow you to perform a number of multi-step RNA-seq analyses automatically.

• Alignment: Bowtie.aligner
• Differential Expression: Cufflinks.cuffdiff
• Genome Annotation: Cufflinks, Cufflinks.cuffcompare, Scripture
• Isoform Detection: Tophat
• RNA Quantitation: Cufflinks, Scripture
• Utilities: Bowtie.indexer, BamToSam, ExprToGct, SamToBam, SortSam
• Visualizers: IGV

RNA-Seq Analysis Tools from the Broad Institute is a post from: RNA-Seq Blog More information about RNA-Seq can be here.