I know there are several links that you can download the genome.
The most popular one should be igenome from illumina.
http://support.illumina.com/sequencing/sequencing_software/igenome.html
And also you can download from tophat website.
But I simply can not download it.
Anyone knows why?
Thanks!
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jolin0701-dy
Download the it from here :
However, I would recommend you to use the gencode annotation (gtf file), download the fasta files and then create the bowtie index. Gencode annotations are more comprehensive and is being used by a lot of big data consortiums TCGA as a standard.
thanks for your link to tophat. It still does not work for me.
But the gencode works...
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whats the error ? E.g.
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz --2016-05-24 11:34:17-- ftp://igenome:password@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz => 'Homo_sapiens_Ensembl_GRCh37.tar.gz' Resolving ussd-ftp.illumina.com... 66.192.10.36 Connecting to ussd-ftp.illumina.com|66.192.10.36|:21... connected. Logging in as igenome ... Error in server response, closing control connection. Retrying.
Define, "simply can not download it." Do you get an error? Does it start and suddenly pause? Does your system administrator suddenly appear and start berating you?
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz
--2016-05-24 11:34:17-- ftp://igenome:password@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz => 'Homo_sapiens_Ensembl_GRCh37.tar.gz' Resolving ussd-ftp.illumina.com... 66.192.10.36 Connecting to ussd-ftp.illumina.com|66.192.10.36|:21... connected. Logging in as igenome ... Error in server response, closing control connection. Retrying.
Talk to your local IT, perhaps you're behind a proxy of some sort.
I second that. This is a local firewall/proxy issue. Looks like they are blocking FTP.