Hello Sheena,

It is odd that this particular genome exists in two versions, with different content, for the same release number/date. Ensemble will update annotation with new releases, but not the reference genome itself unless they also increment the genome build number.


The Zebrafish project page at Ensembl states that UCSC has the latest release, meaning that the genome labeled as "Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)" in Galaxy is expected to be the same as one would create after combining the files in their download area:
http://uswest.ensembl.org/Danio_rerio/Info/Index

But, if there are known differences (perhaps you want different masking or haplotypes/chrY PAR inclusion/exclusion), then combining the data can occur prior to upload into Galaxy or after (both invoke a similar tool):
-- If prior, using unix and the shell "cat" command is one option.
-- If after, then load all chromosomes into your history and use the tool "Text Manipulation -> Concatenate datasets tail-to-head".

Best regards,

Jen
Galaxy team

On 12/6/11 2:31 PM, Scroggins, Sheena wrote:
Thanks for responding. I would like to upload the genome to Galaxy, but I'm not 
sure how to combine all the fa files into one file. The Zebrafish genome from 
Ensembl comes in 27 separate .fa files. How do I combine these so that when I 
upload them to Galaxy, I can use the whole genome as my reference genome?

Thanks,
Sheena

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, November 08, 2011 6:58 AM
To: Scroggins, Sheena
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Uploading Genome from Ensembl

Hello Sheena,

If you concern with using the UCSC version of the database has to do with the 
chromosome naming and downstream Cufflinks analysis using Ensembl's reference 
GTF files, please see #5 on our FAQ, which demonstrates how to modify an 
Ensembl GTF file to be compatible with the UCSC chromosome naming (slight 
changes may be needed for each particular
genome):
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

If there is another reason, please know that custom reference genomes (in fasta 
format) can be uploaded using FTP following this method:
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

Hopefully this helps,

Best,

Jen
Galaxy team

On 11/4/11 2:50 PM, Scroggins, Sheena wrote:
How do I upload the Zebrafish genome from Ensembl to my user history
in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to
map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC
version built in. The Ensembl version is slightly different.
Thanks,
Sheena


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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

 http://lists.bx.psu.edu/

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