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  • miRDeep2 problem

    Dear all,

    Does anyone know that how to convert .sam (mapped file by bowtie) into .arf for as input in miRDeep2.pl ???

    i used sam_reads_collapse.pl and bwa_sam_converter.pl script but got unsatisfactory .arf output.

    find attachment as sample arf while i got correct reads_collapsed.fa file

    Help me please...thanks in advance
    Attached Files

  • #2
    The user has already removed 3' adapters in color space and has mapped the reads against the genome using bwa/bowtie resulting in a sam file. Note that each genome locus to which a read was aligned has to occur in its own line. Otherwise only the first genome locus of each line will be taken! The mapping output file is named mapped.sam. The user wishes to generate the files 'reads_collapsed.fa' and 'reads_collapsed_vs_genome.arf' as input to miRDeep2:

    perl bwa_sam_converter.pl -i mapped.sam -c -o reads_collapsed.fa -a reads_collapsed_vs_genome.arf

    If read ids are already collapsed and in correct miRDeep2 format (eg. ">ABC_1_x10", see file formats) then the sam file just needs to be converted:

    perl bwa_sam_converter.pl -i mapped.sam -a reads_collapsed_vs_genome.arf

    Comment


    • #3
      Problem to launch miRDeep2 in PBS

      Hi all,

      Here i am facing a small problem to launch miRDeep2 into my server by PBS. plz short-out anyone.

      error:

      mkdir mirdeep_runs/run_14_05_2013_t_11_53_28

      Error: Perl PDF::API2 package not found
      Check if the perl PDF::API2 package is correctly installed and all Pathes were set correctly, though right now its running in randfold phase correctly.

      while by simple way (by terminal mode) its running quite well even with PDF::API2 package without any error.

      Note: i also commented to PDF::API2 module inside miRDeep2.pl script to check if other things are ok however yes its okey all except this module.

      i am asking to launch in PBS mode bcz after leaving system, my lab suppose to be off all system by remotely except my cluster server

      please help me,

      Thanks once again and waiting for your kind input.

      Comment


      • #4
        Originally posted by unique379 View Post
        Hi all,

        Here i am facing a small problem to launch miRDeep2 into my server by PBS. plz short-out anyone.

        error:

        mkdir mirdeep_runs/run_14_05_2013_t_11_53_28

        Error: Perl PDF::API2 package not found
        Check if the perl PDF::API2 package is correctly installed and all Pathes were set correctly, though right now its running in randfold phase correctly.

        while by simple way (by terminal mode) its running quite well even with PDF::API2 package without any error.

        Note: i also commented to PDF::API2 module inside miRDeep2.pl script to check if other things are ok however yes its okey all except this module.

        i am asking to launch in PBS mode bcz after leaving system, my lab suppose to be off all system by remotely except my cluster server

        please help me,

        Thanks once again and waiting for your kind input.
        I have the same problem. Please install this software again following mirdeep2 README file, step by step, then you will make it!

        Comment

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