SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
12th International Meeting on Human Genome Variation and Complex Genome Analysis marcowanger Events / Conferences 1 08-29-2011 08:38 PM
Mapping reference genome to ensembl identifier bnfoguy Bioinformatics 0 06-13-2011 06:04 PM
Illumina read naming BaCh Bioinformatics 4 03-04-2011 12:06 PM
BWA building index of full human (ensembl) fails inijman Bioinformatics 4 12-23-2009 05:00 AM
11th International Meeting On HUMAN GENOME VARIATION AND COMPLEX GENOME ANALYSIS HGV2009 Events / Conferences 2 07-24-2009 01:10 AM

Reply
 
Thread Tools
Old 03-03-2011, 01:25 AM   #1
rboettcher
Member
 
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:

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

Join Date: Oct 2009
Posts: 110
Default

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).
ffinkernagel is offline   Reply With Quote
Old 03-03-2011, 04:57 AM   #3
rboettcher
Member
 
Location: Berlin

Join Date: Oct 2010
Posts: 71
Default

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.
rboettcher is offline   Reply With Quote
Old 03-03-2011, 05:32 AM   #4
Bert
Junior Member
 
Location: Cambridge, UK

Join Date: Nov 2009
Posts: 8
Default

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
Bert is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO