[Bioperl-l] Mapping of genome with cytoband

[Smithies, Russell]

Have you tried getting the data from UCSC (or the test site: http://genome-test.cse.ucsc.edu )
If you use Galaxy to get the data then convert to gff, it may save a bit of work.


Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shafeeq rim
> Sent: Thursday, 27 August 2009 11:14 p.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Mapping of genome with cytoband
> 
> Hi,
> 
> I need gene , mrna , cds , sts and exon files as per the mapping with
> cytobands.Lets say for 37.1 version NCBI data. I am checking with the .gbs and
> .gbk files but the genes and other features are not coming across the whole
> chromosome.i.e, for chromosome 1 suppose. When I use the gene coordinates from
> .gbk / .gbs files the locations on chromosome 1 genes show only half way on
> the ideogram graph.
> 
> Thanks
> 
> 
> 
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