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  • mirdeep2 check mirna folding

    Hi,

    i have donwloaded mirdeep2 and i would like to know if my reads (wich are matures sequences) are able to make folding, then i will consider them like microRNA.

    Do you know the command line wich enables this kind of test ?
    Last edited by RTK45; 03-26-2012, 02:29 AM.

  • #2
    In fact,

    i try to use the script excise_precursors.pl:

    excise_precursors.pl genome.fa my_reads.arf -b

    and i obtain this messsage :
    Problem with read format
    Problem with read format
    Problem with read format
    Problem with read format
    Problem with read format
    ...
    However my reads are as in the documentation page :

    .arf
    The arf format is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns. Example line:
    PAN_123456_x969696 21 1 21 ATACAATCTACTGTCTTTCCT chr22 21 46508682 46508702 ATACAATCTACTGTCTTTCCT + 1 mmmmmmmmmmmmmmmmmmmmm
    Any ideas ?

    Comment

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