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Old 03-03-2011, 01:25 AM   #1
Location: Berlin

Join Date: Oct 2010
Posts: 71
Default Ensembl human genome naming pattern

Hi all,
I'm sorry to post this, as I believe it to be a very trivial question. But since it is urgent and I don't have a lot of time to spent on searching the pattern / meaning I'll post anyway.

So here's the question: I have the human genome (GRCh37.58, Ensembl) stored local and I found three files that I can't allocate, the names are:


X and Y as well as the mitochondrium (MT) have their own files, so what chromosomes do these files belong to?

Thanks in advance!

rboettcher is offline   Reply With Quote
Old 03-03-2011, 02:37 AM   #2
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Location: Marburg, Germany

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Ok, these files are not in
how big is each file in that directory of yours?
(And you only named two files - the last two having the same name).
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Old 03-03-2011, 04:57 AM   #3
Location: Berlin

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My mistake, it's chromosome 0, 91 and 92.
Their size differs (chr0 = 20KB, chr91 = 151MB, chr92 = 54MB) but since their not officially included and the nonchromosomal file is missing (haven't seen that before, again my mistake), I suppose they are somewhat linked to it.
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Old 03-03-2011, 05:32 AM   #4
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Location: Cambridge, UK

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As already mentioned, there are no files with these names on our ftp site, so I am afraid I cannot tell you where they come from and what they contain.

Instead of spending a lot of time finding out what they contain, I would suggest you make sure you have all files present in (or alternatively, if you want the newest version of the assembly, and just forget about those three "mystery files" ....

With kind regards,
Bert Overduin, Ph.D.
Ensembl Helpdesk & Outreach
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, United Kingdom
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