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

    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.

  • #2
    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.
    Attached Files
    ---
    http://ugene.unipro.ru

    Comment


    • #3
      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.

      Comment


      • #4
        Originally posted by Quest View Post
        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.
        ---
        http://ugene.unipro.ru

        Comment

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