bed9 Vs bed file format in ENCODE

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deepa kamath

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Oct 26, 2012, 7:28:02 AM10/26/12

to gen...@soe.ucsc.edu

Hi,

   I am trying to download encode methylation data from UCSC site,

   http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/

   I see that there are 2 files .bed and .bed9 file formats available.

   E.g, when I download
   wgEncodeHaibMethylRrbsAg04449UwSitesRep1.bed
   wgEncodeHaibMethylRrbsAg04449UwstamgrowprotSitesRep1.bed9
        These 2 files are exactly same.

   What is the expected difference between these 2 file formats?

Thanks
Deepa

Luvina Guruvadoo

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Oct 26, 2012, 3:55:19 PM10/26/12

to deepa kamath, gen...@soe.ucsc.edu

Hi Deepa,

The bed9 files in this track were preliminary data that has since been replaced. This is indicated by the 'objstatus=replaced' metadata in the downloads metadata file (files.txt) located in this directory: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/. The wgEncodeHaibMethylRrbsAg04449UwSitesRep1.bed is the more recent file.

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group