fasta and bowtie index file download
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7.8 years ago
jolin0701-dy ▴ 100

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!

RNA-Seq • 4.6k views
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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?

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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.

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

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

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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.

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7.8 years ago
Ar ★ 1.1k

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.

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

But the gencode works...

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

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