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miRDeep2 and miRBase

by lucifer7748 (Initiate)
on Jun 02, 2013 at 17:08 UTC ( #1036602=perlquestion: print w/replies, xml ) Need Help??

lucifer7748 has asked for the wisdom of the Perl Monks concerning the following question:

Hi All . I need to check the whole hsa-mir sequences from miRBase by miRDeep 2 , to find if some sequences are not true miRNAs . I have downloaded the sequences in fasta format , and installed miRDeep2 . But I do not know how should I use it to get correct result . Actually the tutorial file couldn't help me also . Please help me . Thanks

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Re: miRDeep2 and miRBase
by Anneq (Vicar) on Jun 02, 2013 at 19:05 UTC

    Maybe the Bio::DB::Fasta CPAN modules might be of use to you.

    Perhaps providing some sample data would help us help you, including true and not true miRNA sequences.

    As well, show us what perl code, if any, you have tried so far.

    If this is not a perl-related question, you are looking in the wrong place for help.

    Anne

Re: miRDeep2 and miRBase
by davido (Cardinal) on Jun 02, 2013 at 19:23 UTC

    I have downloaded the sequences in fasta format, and installed miRDeep2. But I do not know how I should use it to get correct result.

    Is "it" referring to miRDeep2? What is your Perl question?


    Dave

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