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  • gfmgfm
    Member
    • Jun 2010
    • 64

    #1

    small RNA seq analysis

    Hello,

    I have small RNA seq data (plants).

    I did the following:

    1. remove adaptors (with cross match)
    2. create tags

    I now want to check which tags are known miRs and to get a list of miRs instead of tags (and for each miR have a record the relevant tags and total counts).

    Would you use blast for this (tags vs. a database of the miRs)?
    And write scripts that merges tags that "belong" to a miR?

    Any suggestions on the percent identity and alignment length to use?

    Any other suggestions?

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