On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > >> Hi all, >> >> >> >> I have check some useful packages to plot gene chromosome information like >> gene plotter, ideogram and GenomeGraphs. >> >> However, I don't know how to plot microRNA (miRNA) chromosome location. >> >> I would like to see the distribution of some miRNAs in the genome. >> >> >> >> I have known the miRNA chromosome info. >> >> miRNA name chromosome start end >> >> hsa-miR-130b 22 20337592 >> 20337673 >> >> hsa-miR-33a 22 40626894 >> 40626962 >> >> hsa-miR-15b 3 161605069 >> 161605166 >> >> . >> >> >> >> Is there any packages that I provide the location and plotting it out? > > You could create a custom track and upload it to the UCSC genome browser. > > It looks like you got your info about 90% the way to GFF format: > > http://genome.ucsc.edu/FAQ/FAQformat#format3 > > You could tweak your info a bit, then write.table your way to a file you can > upload as a UCSC custom track. See the rtracklayer package for help here. > Is that good enough, or were you looking for something more? And if so, > what? There's the GenomeGraphs library, which is pretty slick, but I'm not > sure if that's really what you're after: > > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html

That helps. Thank you very much. -camper ================================================== Camper Chih-Wei Liu National Cheng Kung University, Tainan, Taiwan Department of Computer Science and Information Engineering Intelligent Information Retrieval Lab: IIR Lab camper at cad.csie.ncku.edu.tw -----Original Message----- From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Sent: Tuesday, October 28, 2008 9:14 AM To: Camper (Chih-Wei Liu) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] How to plot microRNA chromosome location Hi, On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote: > Hi all, > > > > I have check some useful packages to plot gene chromosome > information like > gene plotter, ideogram and GenomeGraphs. > > However, I don't know how to plot microRNA (miRNA) chromosome > location. > > I would like to see the distribution of some miRNAs in the genome. > > > > I have known the miRNA chromosome info. > > miRNA name chromosome start end > > hsa-miR-130b 22 20337592 > 20337673 > > hsa-miR-33a 22 40626894 > 40626962 > > hsa-miR-15b 3 161605069 > 161605166 > > . > > > > Is there any packages that I provide the location and plotting it out? You could create a custom track and upload it to the UCSC genome browser. It looks like you got your info about 90% the way to GFF format: http://genome.ucsc.edu/FAQ/FAQformat#format3 You could tweak your info a bit, then write.table your way to a file you can upload as a UCSC custom track. Is that good enough, or were you looking for something more? And if so, what? There's the GenomeGraphs library, which is pretty slick, but I'm not sure if that's really what you're after: http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html Hope that helps, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College of Cornell University http://cbio.mskcc.org/~lianos