Hi, On Sun, Mar 24, 2013 at 11:55 PM, Asma rabe <asma.rabe at="" gmail.com=""> wrote: > ---------- Forwarded message ---------- > From: Asma rabe <asma.rabe at="" gmail.com=""> > Date: Sat, Mar 23, 2013 at 9:08 AM > Subject: EdgeR-tophat > To: Bioconductor at r-project.org > > > Hi All, > > I have RNA-Seq data which i mapped and used tophat for mapping splice > junctions,I would like to use EdgeR for identifying differentially > expressed genes. > Do you have an idea if i can use tophat out put file as input for edgeR? edgeR requires a matrix or read counts as input -- rows are features (likely "genes" for you), columns are the counts of your features across different samples. As far as edgeR is concerned, the onus of creating this count matrix from your aligned reads is on you. The easyRNASeq package (for one) has ways to summarize read counts over genes into a form suitable for differential expression analysis. There are also other ways to do so. Martin recently posted a link to a ~ 100 page tutorial covering a large variety of analyses tasks for sequencing data using a variety of bioconductor packages that will likely be worth your time to read through: http://bioconductor.org/help/course- materials/2013/SeattleFeb2013/IntermediateSequenceAnalysis2013.pdf HTH, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact