fasta and bowtie index file download

Question

[jolin0701-dy]

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!

[Devon Ryan]

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?

[jolin0701-dy]

wget ftp://igenome:[e-mail]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz

--2016-05-24 11:34:17-- ftp://igenome:[e-mail]/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.

[Devon Ryan]

Talk to your local IT, perhaps you're behind a proxy of some sort.

[GenoMax]

I second that. This is a local firewall/proxy issue. Looks like they are blocking FTP.

[GouthamAtla]

whats the error ? E.g.

wget ftp://igenome:[e-mail]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz

[jolin0701-dy]

wget ftp://igenome:[e-mail]/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz --2016-05-24 11:34:17-- ftp://igenome:[e-mail]/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.

Answer 1

[Ar]

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.

[jolin0701-dy]

thanks for your link to tophat. It still does not work for me.

But the gencode works...

[Ar]

I would then ask your IT admin. I think there could be firewall/proxy issue.