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Old 01-08-2014, 01:02 AM   #1
Parharn
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Default iGenome S. pombe builds

Hi,
I am wondering what are "builds" in iGenomes data base.
I work on S.pombe. I don't know which build to use for my analysis. EF1 or EF2?

The link to the webpage is here: http://support.illumina.com/sequenci...e/igenome.ilmn

Thanks,
Parham
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Old 01-08-2014, 03:23 AM   #2
GenoMax
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EF2 should be a later genome build than EF1 (following the convention). So you would probably want to use EF2.

Ensembl appears to have dropped EF* designations for the yeast genomes with the latest pombe genome now called "ASM294v2": http://fungi.ensembl.org/Schizosacch...be/Info/Index/
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Old 01-08-2014, 03:55 AM   #3
Parharn
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Thanks, but the EF2 contains all the index files for bowtie and stuff. The ASM294v2 seems that contains only the reference files.
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Old 01-08-2014, 04:01 AM   #4
GenoMax
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EF2 version from iGenomes would be convenient to use since it is cleaned up (names etc) and has all the indexes/annotations pre-built. For most applications that would be just fine (unless you are doing something that requires the latest genome build. Then you would have to download the genome and build the index yourself).
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Old 01-08-2014, 04:21 AM   #5
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Got it, thanks GenoMax!
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