Hello list members, I usually work in R environment for most of my projects. I am interested in using R/Bioconductor to detect small RNA species in Illumina DGE data. After reviewing available Bioconductor packages, I have an impression that there is no establisted pipeline to do that (is that true?). I'd like to hear from the list members who successfully used Bioconductor resources for this purpose. Thank you, Oleg Moskvin

Hi Oleg, On Wed, Oct 13, 2010 at 5:39 PM, Oleg Moskvin <moskvin at="" wisc.edu=""> wrote: > Hello list members, > > I usually work in R environment for most of my projects. I am interested in using R/Bioconductor to detect small RNA species in Illumina DGE data. After reviewing available Bioconductor packages, I have an impression that there is no establisted pipeline to do that (is that true?). I'd like to hear from the list members who successfully used Bioconductor resources for this purpose. When you're talking about DGE, are you talking about the SAGE-like tag profiling protocol from Illumina? If so, then I'm pretty sure there isn't an established pipeline. I've been developing some packages that deal with this type of data to take it from raw reads -> stripped adapters -> alignment -> annotated tags. I'd like to add it to the bioconductor-package universe in due time, but it's not really ready for public consumption. I'm a bit surprised that you're using DGE (the type I'm thinking of) to detect small RNAs, though, so maybe we're not talking about the same thing (?). -- 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

On Wed, Oct 13, 2010 at 5:39 PM, Oleg Moskvin <moskvin@wisc.edu> wrote: > Hello list members, > > I usually work in R environment for most of my projects. I am interested in > using R/Bioconductor to detect small RNA species in Illumina DGE data. After > reviewing available Bioconductor packages, I have an impression that there > is no establisted pipeline to do that (is that true?). I'd like to hear from > the list members who successfully used Bioconductor resources for this > purpose. > > Hi, Oleg. Not sure what you mean by Illumina DGE data, but the first place to start is to determine if the protocol used in sequencing even captures small RNA species. If so, does the alignment method capture them if they are present in the sequencing data? If the answer to both is true, then you could potentially use the same counting infrastructures as are used for RNA-seq or for ChIP-seq (peak-finding). As with many sequencing applications, though, the approach will depend on the details of the experiment. Perhaps some more detail would be helpful. Sean [[alternative HTML version deleted]]

Hi Sean, Thank you for the hints. I see what you mean. Since ChiP-seq workflow is inevitable here and I don't have experience with that, I should rephrase and narrow down my question to "which Bioconductor/R tools are the best at the moment to genome coverage visualization and differential expression test, if we start, say, from read counts table generated with ShortRead and a ByPos_MIndex object of genome hits generated with Biostrings"? Thank you, Oleg From: Sean Davis Sent: Wednesday, October 13, 2010 6:56 PM To: Oleg Moskvin Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Illumina DGE => sRNA detection pipeline On Wed, Oct 13, 2010 at 5:39 PM, Oleg Moskvin <moskvin@wisc.edu> wrote: Hello list members, I usually work in R environment for most of my projects. I am interested in using R/Bioconductor to detect small RNA species in Illumina DGE data. After reviewing available Bioconductor packages, I have an impression that there is no establisted pipeline to do that (is that true?). I'd like to hear from the list members who successfully used Bioconductor resources for this purpose. Hi, Oleg. Â Not sure what you mean by Illumina DGE data, but the first place to start is to determine if the protocol used in sequencing even captures small RNA species. Â If so, does the alignment method capture them if they are present in the sequencing data? Â If the answer to both is true, then you could potentially use the same counting infrastructures as are used for RNA-seq or for ChIP-seq (peak- finding). Â As with many sequencing applications, though, the approach will depend on the details of the experiment. Â Perhaps some more detail would be helpful. Â Sean [[alternative HTML version deleted]]