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Question: Missing genome in Tophat2
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gravatar for ashamchu
4.2 years ago by
ashamchu • 10
Canada
ashamchu • 10 wrote:

Hi Galaxy Team,

Is there any way to get the latest Zebrafish (Danio rerio) genome added to the reference genome options in Tophat2?

Thank you!
tophat2 indexes • 1.0k views
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modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by ashamchu • 10
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gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This genome is already on our next list of genomes to process, the card is here: http://trello.com/c/YqRsZnFI

Meanwhile, you can use the genome right now as a Custom Reference Genome.
http://wiki.galaxyproject.org/Support#Custom_reference_genome

In short, load the genome in fasta format into your history and use it with the tool settings to use a reference genome "from the history".

The "danRerN" genomes on the public server are sourced from UCSC here: 
http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish

Or you can obtain our exact version from our rsync server:
http://wiki.galaxyproject.org/Admin/UseGalaxyRsync

 

Best, Jen, Galaxy team
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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