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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
Good Afternoon Sheena:
Can you please explain what is different between the Ensembl and UCSC
Zebrafish Zv9 genome sequences ?
--Hiram
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
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
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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