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  • Randfol in miRDeep2

    Hello all,
    I am trying to get miRDeep 2 to work with my data.
    Everything goes fine with mapping, collapsing, etc.
    When I try to run the mirDeep2.pl using the script
    Code:
    perl mirDeep2.pl collapsed.fa Genome.fa collapsed_vs_Genome.arf none none none
    the initial process work fine. Until Randfold! The pipeline stops in "computing randfold p-values". One nucleus stay at 100% activity.
    How long is this process? Here, 2 h and still counting.
    Thank you for your help.
    Charley

  • #2
    Dear all.
    I Just realized that the process is quite long. The data analysis (4 Gb of fasta files) runned in 3 hours in a I5 processor with 8gb RAM.
    Thank you all.
    Charley

    Comment


    • #3
      RNAfold is most time-consuming task in predicting miRNAs from deep sequencing. All current predicting tools miRDeep, miRTRAP, MIReNA, miRDeep* and etc. use similar RNA secondary structure prediction algorithm. but it is not necessary to use big memory for preducting RNA secondary structure.

      Comment


      • #4
        Hi,

        I'm having trouble making randfold 2.0. I have the SQUID libraries but get this message when making randfold:

        Code:
        -bash-4.1$ make
        gcc -O3 -I.  -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid 
        randfold.c:24:18: error: squid.h: No such file or directory
        randfold.c:26:23: error: sre_random.h: No such file or directory
        randfold.c: In function 'main':
        randfold.c:30: error: 'SQFILE' undeclared (first use in this function)
        randfold.c:30: error: (Each undeclared identifier is reported only once
        randfold.c:30: error: for each function it appears in.)
        randfold.c:30: error: 'sqfp' undeclared (first use in this function)
        randfold.c:38: error: 'SQINFO' undeclared (first use in this function)
        randfold.c:38: error: expected ';' before 'sqinfo'
        randfold.c:89: warning: incompatible implicit declaration of built-in function 'strcpy'
        randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this function)
        randfold.c:100: error: 'sqinfo' undeclared (first use in this function)
        randfold.c:103: warning: incompatible implicit declaration of built-in function 'malloc'
        randfold.c:103: warning: incompatible implicit declaration of built-in function 'strlen'
        randfold.c:136: warning: incompatible implicit declaration of built-in function 'fabs'
        randfold.c:158: warning: incompatible implicit declaration of built-in function 'free'
        make: *** [randfold] Error 1
        I am quite a novise when it comes to these things. Should I perhaps configure the makefile?

        Comment


        • #5
          rndfold in mirdeep 2

          I recently done small RNA sequencing of my endocrine tumour samples. I got result analysis with Mirdeep2 . I am not master in bioinformatics so , i outsourced the analysis. The company have predicted some novel micrornas. They have used mirdeep2 software for predicting novel microRNA.
          I am facing problem in selecting novel microRNAs from small RNA sequencing. Is it necessary to have high mirdeep2 score with high mature read count. Those sequence with high mirdeep2 score ( like 3168) & mature read count (456) have non significant RANDFOLD p value. I am confused in this part.
          Basically , I want to validate the results using PCR. But i am facing alot of problem in selecting top 5 novel microRNAs. I read in mirdeep2 documentation in which the score cut was from -10 to 10.
          Please guide me regarding mirdeep2 software and please help me its parameters for selecting novel microRNA.I will be very thankful to you.
          thanks.
          Regards

          Comment

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