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Dreaded (because unresolved) bad_alloc error Aurelien Mazurie Bioinformatics 2 09-26-2011 09:23 AM

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Old 07-26-2011, 07:32 PM   #1
yaximik
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Location: Oregon

Join Date: Apr 2011
Posts: 205
Unhappy Still unresolved question?

Hi everyone,

I was browsing previous topics in hope to find a way to generate GoldenPath-type annotation file (AGP format?) to feed into GS Reference Mapper, similar to refGene.txt that can be dowloaded from UCSC Genome Browser site (for human genome). A few questions like conversion of a GenBank annotatoion file still remain unanswered, but these are one year old inquiries.

Basically, I am looking for a way to generate GoldenPath-type refGene.txt or snp130.txt for bacterial genomes using GenBank entires. I found a tool to generate .GFF file from GenBank, which can be fed in Genome Browser to make custom tracks, but it is not obvious that something on the site can be used for conversion to the GoldenPath format. GS Reference Mapper seems to take only GoldenPath annotation files, but not GFF. Are any further developments on the conversion problem?
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