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  • RNA-seq data sample

    Hello,

    I need some RNA seq data & the coresponding genome annotation.
    I'm new to the business and am trying to develop a segmentation method.

    I searched the web but did not find untill this moment any good data.
    I don't need full genome but just >10MB sample.

    Thank you,

    Bogdan

  • #2
    Short Read Archive

    Hi,

    you could try the Short Read Archive (http://www.ncbi.nlm.nih.gov/sra), although their datasets are normally in files of at least 500 Mb . . . you could just download some and then extract a reasonable subset of reads from the files (you might have to familiarize yourself a little bit with the formats beforehand).

    I don't exactly know what you are trying to do, but if your method is meant to work on real-life data you should not restrict yourself too much in the size (like the max. 10 Mb that you mentioned), because you might end up developing something that works well on toy examples but does not scale well for the amounts of data a real-life RNA-Seq experiment might produce.

    Cheers

    "You are only young once, but you can stay immature indefinitely."

    Comment


    • #3
      Thanks, I'll try to get the data from the ncbi site.
      And thanks again for the advice you gave me. I want to use a small smaple just to allow my machine to work. For the moment it can't handle big data.

      Bogdan

      Comment


      • #4
        The point made by Dethecor is a good one. There is nothing particularly unique about the substance of next-gen sequencing data itself. What is unique and remarkable about it is the sheer volume of it. What is needed most by the field is the ability to rapidly process these huge data sets without excessive memory usage. Start working with large data sets right away. In addition to SRA you can also find RNA-Seq data in GEO. They have a better interface for searching their data archive (IMHO).

        For example ... if you go to the following link, select 'GEO DataSets' from the drop down menu, and use 'RNA-Seq' as your search term you currently get 78 RNA-Seq data sets deposited in GEO.
        http://www.ncbi.nlm.nih.gov/sites/entrez

        All kinds of interesting test data sets to play around with in there...

        Comment

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