[BioC] How to plot microRNA chromosome location
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Tue Oct 28 02:13:30 CET 2008
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
> 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
> hsa-miR-33a 22 40626894
> hsa-miR-15b 3 161605069
> 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
It looks like you got your info about 90% the way to GFF format:
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:
Hope that helps,
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University
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