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  • vebaev
    Senior Res.
    • Oct 2008
    • 112

    #1

    small seq reads in GEO? how to map them?

    Hi all,
    this is my first post here
    And as slowly entering in deep-seq world I was wandering how to use a data in GEO datasets NCBI, for Example that one from Illumina:


    Is downloading "full table" will dive me an untrimmed from adaptors pure reads ready for mapping or?
    At the bottom they provide fastaq format but I think is untrimmed? and how to trimm adaptors if I do not know the adaptors seq?

    Can I just "Download full table..." and map the seqs to reference genome?

    As a finale goal I want/need to generate a GFF file with locations of these small RNAs
    sorry for my newbies questions but I feel like a pin in the ocean of info

    Thanks!
    ------------
    SMART - bioinfo.uni-plovdiv.bg

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