Hey Martin Thats exactly what I intended but sent it to general R list. Will post it again. Thanks for checking.
-A On Mon, Oct 24, 2011 at 2:32 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > On 10/24/2011 02:23 PM, Abhishek Pratap wrote: > >> Hi All >> >> I am wondering if people based on their experience could share what >> methods >> one could use to compare two gff/gtf files. The reason why I want to do so >> is that we have constructed a RNA-Seq based transcriptome and would like >> to >> compare it with reference transcriptome we had from in-silico approaches. >> Ideally we are looking to find out >> >> 1. new genes we see >> 2. transcripts where the start/end side is changed (upstream/downstream) >> 3. possible gene fusions may be because in-silico approaches were not >> correct >> >> I know some of these could be resolved with BedTools but just wondering if >> Bioconductor has anything specific built in coz each time it pleasantly >> surprises me. >> > > Hi Abhi -- > > better to ask on the Bioconductor mailing list > > http://bioconductor.org/help/**mailing-list/<http://bioconductor.org/help/mailing-list/> > > where people will point to rtracklayer to import() gff files, and > GenomicRanges to do the types of comparisons you're interested in. These > will generally be fun and performant tools. > > Martin > > >> Thanks! >> -Abhi >> >> [[alternative HTML version deleted]] >> >> ______________________________**________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> >> PLEASE do read the posting guide http://www.R-project.org/** >> posting-guide.html <http://www.R-project.org/posting-guide.html> >> and provide commented, minimal, self-contained, reproducible code. >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
