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Question: How to extract genes.gtf file from uncompressed gz file
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gravatar for amaheras7091
2.5 years ago by
amaheras7091 • 10
amaheras7091 • 10 wrote:

Hi,

I am trying to use the DanRer10 UCSC zebrafish genome file found on the illumina website under iGenomes in my RNA-seq Cufflinks workflow. The file downloaded as a compressed tar.gz file, so I uncompressed it with 7-zip (a program downloaded from the internet) which gave me an uncompressed gz file I believe. However, now I'm unsure as to how to get just the genes.gtf file to use in galaxy.

Thank you so much for any and all help :)
rna-seq cufflinks galaxy • 1.1k views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by amaheras7091 • 10
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To fully extract the archive into the same working directory as the original file, use this command: 

tar zxvf file.tar.gz

The genes.gtf file will be nested in the annotation directory. Upload just this file to Galaxy for most use cases. The other files provide additional support information/annotation for the specific build and can be loaded as needed.

Best, Jen, Galaxy team
ADD COMMENT • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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