Uploading Genome From Ensembl

Question: Uploading Genome From Ensembl

7.1 years ago by

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

galaxy • 1.8k views

ADD COMMENT • link •

modified 7.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Scroggins, Sheena • 30

7.1 years ago by

Hiram Clawson • 260

Hiram Clawson • 260 wrote:

Can you clarify what is different between the Zv9 version of the UCSC Zebrafish and the Zv9 version of the Ensembl Zebrafish genome ? They both appear to have the identical number of 1,412,464,843 nucleotides. --Hiram To: galaxy-user@bx.psu.edu Subject: [galaxy-user] Uploading Genome from Ensembl How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? Iâm 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

ADD COMMENT • link written 7.1 years ago by Hiram Clawson • 260

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 7.0 years ago by Hiram Clawson • 260

Please log in to add an answer.

Similar posts • Search »