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  • miRNAkey

    Hi All,

    I am referring to your publication "miRNAkey: a software for microRNA deep sequencing analysis" in Bioinformatics.

    I have few questions regarding the output of the miRNAkey. Specifically I am referring to an Excel file for Differential Expression Table. For most of miRNA, there are two rows (for examples hsa-let-7a and hsa-let-7a*), what is the difference between these two miRNA? Also, it generates fold-change value of +Infinity for positive two number (for example fold-change for RPKM1=0.801 and RPKM2=591.740 is +Infinity). Is it possible to convert mapped .sam file to .bed format to visualize the data in the UCSC genome browser?

    I really appreciate your help on these issues.

    Thanks,

    Rakesh

  • #2
    A microRNA is processed from a precursor miRNA (pre-miR). From a pre-miRNA, two miRNA are processed, the mature and the star.

    So hsa-let-7a and hsa-let-7a* are processed from the same pre-miR (http://www.mirbase.org/cgi-bin/mirna...?acc=MI0000060).



    To convert .sam to .bed --> http://seqanswers.com/forums/showthread.php?t=2446

    For the foldchange, I don't use miRNAkey..

    Nico

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    • #3
      Hi Nico,

      Thanks for your detail response. I tried to use samtools and bedtools to convert .sam files to .bed files but I used human genomes 19 as reference. But I believe it might be better to use miRBase instead. Do you have any other suggestions?

      Best wishes,

      Rakesh

      Comment


      • #4
        miRNAkey error

        Alignment summary:
        Total reads: 736516
        Mapped reads: 255576
        Uniquely mapped reads: 249567 (97.6% of mapped reads)
        Multiply mapped reads: 6009 (2.4% of mapped reads)


        Error message:
        .....
        Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 181, <$BWA_INPUT> line 738143.
        Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 200, <$BWA_INPUT> line 738143.
        .....
        Differential Expression Analysis summary:
        A total of 2 different miRNAs were expressed in the two samples


        its the same error at line 181 and 200 for all the samples ; and all samples show only two differentially expressed miRNAs

        (i tried with Bwa.0.5.7 and 0.5.9 ): both has same errors

        please do suggest me what went wrong and how to over come this error?
        Last edited by gpcr; 03-28-2012, 09:13 AM.

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