Ensembl human genome naming pattern

[rboettcher]

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:

Homo_sapiens.GRCh37.58.dna.chromosome.0.fa
Homo_sapiens.GRCh37.58.dna.chromosome.91.fa
Homo_sapiens.GRCh37.58.dna.chromosome.91.fa

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

Thanks in advance!

Regards

[ffinkernagel]

Ok, these files are not in ftp://ftp.ensembl.org/pub/release-58...o_sapiens/dna/
how big is each file in that directory of yours?
(And you only named two files - the last two having the same name).

[rboettcher]

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.

[Bert]

Hi,

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 ftp://ftp.ensembl.org/pub/release-58...o_sapiens/dna/ (or alternatively, if you want the newest version of the assembly, ftp://ftp.ensembl.org/pub/release-61...o_sapiens/dna/) 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