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.
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smithkthedale •
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.
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.
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.
Yes, the file is out of my trash and on my desktop now now how do I download it to linux?
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.
please help
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
This is a good place to start: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/
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Also, should it be in a .zip file on my desktop?
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?
Your link doesn't have any files in it.