What is the command to download GTF from NCBI
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24 months ago

What is the command to download: https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/218851/ GTF File. Mac downloads won't open...so need a way to wget (or another alternative) the gif file in linux.

Please help and write the command, so that I can open the gtf in linux.

ncbi gtf linux • 2.7k views
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Also, should it be in a .zip file on my desktop?

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If you have disabled automatic zip archive expansion on your Mac, I expect you will see a Zip file downloaded to your default download location; perhaps the "Downloads" folder?

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Yes, I am using linux command line. Here is the gtf file I want to appear in my linux cd. Is there no type of command like wget?

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Your link doesn't have any files in it.

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24 months ago

From the command line on your linux machine:

curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets'
chmod +x datasets

./datasets download genome accession GCA_002738505.1 --filename dataset.zip
unzip dataset.zip

See here for more on the datasets tool.

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If you only need the annotation file then add the following options to command shown by @jared.

--exclude-protein          exclude protein.faa (protein sequence file)
--exclude-rna              exclude rna.fna (transcript sequence file)
--exclude-seq              exclude genomic.fna (genomic sequence file)
--include-gtf              include genomic.gtf (gtf annotation file), if available

If GTF files are not available then GFF file will be only option.

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24 months ago
vkkodali_ncbi ★ 3.7k

There's a known issue with using Safari on Macs to download these data as described here: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/troubleshooting/mac-zip-bug/

Is this what you are noticing? If so, please follow the workaround described in the above link.

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Yes, the file is out of my trash and on my desktop now now how do I download it to linux?

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It depends on how you are connected to your linux machine. Are you accessing it through a command line from your Mac? If so, you can either directly download the data using datasets command line tool on your linux machine or copy the files from your Mac using something like an SFTP utility.

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please help

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I am accessing command line from my Mac. Can you please explain how to use the datasets command line tool? I am a complete newbie

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