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Old 09-19-2012, 02:47 PM   #1
JQL
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Default iGenome ftp site

Hi,

Sorry for this naive question. I would like to get the GTF files from Illumina's iGenome ftp site, but don't have access. I can download from http://cufflinks.cbcb.umd.edu/igenomes.html

but how to access from a linux server? It prompted for user name and pwd which were denied.

thanks!
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Old 09-19-2012, 03:10 PM   #2
Richard Finney
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Worked for me:
ftp ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com

I did this ...
-bash-3.00$ ftp
ftp> open ussd-ftp.illumina.com
Connected to ussd-ftp.illumina.com.
220 EFT Server 6.4.1 Build 12.19.2011.1
500 Protocol not supported.
500 Protocol not supported.
KERBEROS_V4 rejected as an authentication type
Name (ussd-ftp.illumina.com:finneyr): igenome
331 Password required for igenome.
Password: (note, enter G3nom3s4u )
230 Login OK. Proceed.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> pwd
257 "/" is current folder.
ftp> cd Homo_sapiens
250 Folder changed to "/Homo_sapiens".
ftp> cd NCBI/build37.1
250 Folder changed to "/Homo_sapiens/NCBI/build37.1".
ftp> ls
227 Entering Passive Mode (66,192,10,36,216,48).
150 Opening ASCII mode data connection for file list.
-r--r--r-- 1 user group 16620139308 May 14 19:04 Homo_sapiens_NCBI_build37.1.tar.gz
226 Transfer complete. 91 bytes transferred. 91 bps.
ftp>
....

Better yet just use "wget".

Search for wget for more info.
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Old 09-19-2012, 03:56 PM   #3
JQL
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Thank you. I thought that was what I entered. I will try again tomorrow.
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Old 09-20-2012, 07:41 AM   #4
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Both wget and get worked.

is wget generally preferred becaused it downloads faster?
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Old 09-20-2012, 07:49 AM   #5
Richard Finney
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wget is very convenient for scripting.
For instance you can scrape the page, filter out the URLs, pick the ones you want and slap a "wget " in front and pipe it to a shell. Tricky but easily do-able with with a little experience.

ftp and (sftp with -b parameter) is scriptable, too.

They are both the same speed as they're written in C and implement the same protocol (though wget does support other protocols, notably the http protocol). Any difference you see are probably network congestion or the result of I/O caching.

Last edited by Richard Finney; 09-20-2012 at 07:54 AM.
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Old 09-20-2012, 08:05 AM   #6
JQL
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thanks Richard.
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Old 09-11-2013, 12:18 AM   #7
Etherella
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Sorry for reviving this old topic, but I cannot connect to ussd-ftp.illumina.com. It says : connection reset by peer.

How can I download the human genome hg19?
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Old 09-11-2013, 04:11 AM   #8
GenoMax
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Quote:
Originally Posted by Etherella View Post
Sorry for reviving this old topic, but I cannot connect to ussd-ftp.illumina.com. It says : connection reset by peer.

How can I download the human genome hg19?
Are you behind an institutional firewall that is preventing you from downloading?
The iGenomes/Illumina server is up and available.

If you only need the hg19 sequence then you can get it from other locations:

UCSC: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/
Ensembl: ftp://ftp.ensembl.org/pub/release-73...o_sapiens/dna/
NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/
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Old 09-11-2013, 04:16 AM   #9
Etherella
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Thanks a lot!
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Old 09-18-2013, 06:01 AM   #10
lucas81
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Dear all, I cannot access the iGenome ftp server too. Is there some problem?

Thanks
Luca
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Old 09-18-2013, 06:09 AM   #11
GenoMax
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Quote:
Originally Posted by lucas81 View Post
Dear all, I cannot access the iGenome ftp server too. Is there some problem?

Thanks
Luca
Server is up and available. Local firewall may be preventing you from reaching the site.
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Old 09-18-2013, 06:15 AM   #12
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Dear GenoMax I tried from different computers in different institution, so I don't think is a problem of firewall... have you tried to download this? ftp://ussd-ftp.illumina.com/Mus_musc..._GRCm38.tar.gz

Best and thanks for your prompt reply

Luca
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Old 09-18-2013, 06:28 AM   #13
GenoMax
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Quote:
Originally Posted by lucas81 View Post
Dear GenoMax I tried from different computers in different institution, so I don't think is a problem of firewall... have you tried to download this? ftp://ussd-ftp.illumina.com/Mus_musc..._GRCm38.tar.gz

Best and thanks for your prompt reply

Luca
The link you posted is working for me (with right login/password, see below).

You are trying to download a genome that is not listed on the iGenomes site (http://cufflinks.cbcb.umd.edu/igenomes.html). If you look at one of the existing download links at the igenomes site you will see the account name/password (embedded in the link) that you need to use for the FTP site (which will work for the link above).

Post #2 in this thread has the login information you need.

Last edited by GenoMax; 09-18-2013 at 06:35 AM.
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Old 09-18-2013, 07:00 AM   #14
lucas81
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Default solved (I hope)

Quote:
Originally Posted by GenoMax View Post
The link you posted is working for me (with right login/password, see below).

You are trying to download a genome that is not listed on the iGenomes site (http://cufflinks.cbcb.umd.edu/igenomes.html). If you look at one of the existing download links at the igenomes site you will see the account name/password (embedded in the link) that you need to use for the FTP site (which will work for the link above).

Post #2 in this thread has the login information you need.
Many thanks for your advice. We have some IP problem apparently. We managed accessing a computer in another city(!). Many thanks again!

Luca
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