Im trying to learn how to use filezilla to connect to NCBI databases for easier download.
I found the RefSeq: ftp.ncbi.nlm.nih.gov/refseq/
But when i try to quickconnect to this via filezilla i get the following message:
"this server does not support FTP over TLS filezilla if you continue, your password and files will be sent in clear over the internet"
Sending my files and password clear over the internet sound like a bad idea. -Am i doing something wrong or have i simply misunderstood how to connect to an FTP safely.
Any guides to downloading databases (not one file at a time) are also very welcome.
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Jakoemi •
1 answer
But when i try to quickconnect to this via filezilla i get the following message: "this server does not support FTP over TLS filezilla if you continue, your password and files will be sent in clear over the internet"
They are using anonymous FTP connections for public data. Therefore, you can use any user/password or none at all, not your local account and password. By convention, you may use username: anonymous and your email address as password. You can use these settings in your FileZila client. This in case you still want to use the plain old FTP protocol without any transport layer security.
Otherwise, have a look at NCBI Datasets.
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try to use https instead of ftp. https://ftp.ncbi.nlm.nih.gov/refseq/
That gives me a syntax error
It says that valid protocols are: ftp:// sftp:// ftps:// or ftoes://
Simply use any web browser (or click on the link above). You do not need
filezilla.But that only allows me to look through the files. If i want to run it in any kind of program i need it downloaded so i can do some indexing and stuff. - right?
use wget or curl
https://linux.die.net/man/1/wget
biostars wants this text
Does wget allow me to pull down the whole directory? Not that i need everything, but in theory?
I only manage to find guides to get a single file at a time. This would take ages.
https://stackoverflow.com/questions/273743/
I think this answers at least some of my questions, thanks.
Before we go in too deep would you mind providing some information about your expertise? Are you a computational scientist looking to get into biological data/databases?
BTW: There are already biological databases that are preformatted (e.g. BLAST) that will allow you to do searches against.
Ive used some of these online access point before. Like i know how to run a BLAST on the website.
But now i am trying to build a more high throughput system and cant go c/p every singe file.
What is it that you want download? Genome sequence/proteins?
Any kind of sequence database, im just trying to understand the concept
Can you be more specific? What is it that you want to do with such data?
i replied to your similar question in the other tread.