Dear all, I am trying to analyze RNA seq data with goseq but I have a problem: mm10(the reference genome that I am using for my experiment) is not supported by goseq. The last version supported by goseq is mm9. Can you help me to annotate mm10 RNA seq data with goseq? The version of my goseq is: 1.8.0. Thanks in advance. Regards, Vincenzo [[alternative HTML version deleted]]

Hi, On Wed, Jan 30, 2013 at 4:10 AM, Vincenzo Capece <vivo0304 at="" gmail.com=""> wrote: > Dear all, > I am trying to analyze RNA seq data with goseq but I have a problem: > mm10(the reference genome that I am using for my experiment) is not > supported by goseq. The last version supported by goseq is mm9. > Can you help me to annotate mm10 RNA seq data with goseq? > The version of my goseq is: 1.8.0. > Thanks in advance. You "just" need to annotate your read count values with the length of the transcript it is coming from, right? This can easily be done with a GenomicFeatures database built from the annotation source you used to tally the reads/gene(or transcript). There are ones already built for you here: http://bioconductor.org/packages/release/BiocViews.html#___AnnotationD ata Namely the following packages: * TxDb.Mmusculus.UCSC.mm10.ensGene * TxDb.Mmusculus.UCSC.mm10.knownGene Or you can build your own if you didn't use the ensemble of ucsc annotations. If you're not already familiar with the functionality provided in the GenomicFeatures package, I'd encourage you to read through its documentation (vignettes) -- it's extremely helpful. Once you do so, you'll find it very easy to calculate the width of your transcripts (or portions of them) as you see fit. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Vincenzo Capece <vivo0304 at="" ...=""> writes: > > Dear all, > I am trying to analyze RNA seq data with goseq but I have a problem: > mm10(the reference genome that I am using for my experiment) is not > supported by goseq. The last version supported by goseq is mm9. > Can you help me to annotate mm10 RNA seq data with goseq? > The version of my goseq is: 1.8.0. > Thanks in advance. > Regards, > > Vincenzo > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Vincenzo, Indeed it looks like genLenDataBase has not been updated to support mm10, so I will try to rectify this. In the mean time, I have updated goseq so that it attempts to download the gene length information from UCSC if it's missing from genLenDataBase. This is a bit slower, but should work just as well. The fix will be in goseq version 1.11.2 onwards. Email me if you want the source code sooner than it becomes available on http://bioconductor.org/packages/2.12/bioc/html/goseq.html. Which annotation are you using by the way? Cheers, Nadia.