How to download annotated reference genome for CCL Bio GWB and others

[Quest]

Hi, I am a molecular biologist trying to analyze my ChIP-seq (and mRNA-seq later) by commercial software, such as Genomic WB (CCL Bio) and NextGene (SoftGenetics). I am having very hard time regarding to getting annotated reference genome.
1)By downloading NC_#### file through Genomic WB: very slow and disappeared (or not useable) after saving it in the the WB's navigation area.

2)Trying to find a ftp site for fast download, but I am still clueless about which URL and which files I should download.

At this moment, I would like to have mm8, mm9, hg18 and hg19, Could anybody kindly give me advice? Thanks in advance.

[mfursov]

You can try automate downloading Genbank NC_** records with UGENE software (it's free) and use it later with any other tool you like.

See the screenshot.

[Quest]

Thank you mfursov for the reply. Hm... but Maybe because I did it wrong, UGENE only "access" the remote database but without really downloading any file for me.

By the way, what is the file format of NC_#### file?

Although the commercial software is getting more friendly for a molecular biologist, it's still hard to start :-( Any help is appreciated.

[mfursov]

Thank you mfursov for the reply. Hm... but Maybe because I did it wrong, UGENE only "access" the remote database but without really downloading any file for me.

By the way, what is the file format of NC_#### file?

Although the commercial software is getting more friendly for a molecular biologist, it's still hard to start :-( Any help is appreciated.

Here are the answers:

1) The file is downloaded to your computer and placed to the ".UGENE_downloaded" in your home folder (c:\documents and settings\<user_name> or /home/<user_name>). You can access it directly as file or view/export it with UGENE interface.

2) NC_#### file has Genbank file format and is an entry of NCBI database. The file usually contains the sequence and annotations for the sequence.