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  • Error in MIREAP

    Hello.

    I'm trying to run MIREAP to predict novel miRNAs in my dataset.
    However, when I run the script, the following message appears:

    Can't use an undefined value as an ARRAY reference at ./bin/mireap.pl line 714.

    When I run the test file, the message does not appear and the result are correct. So I'm guessing the problem is my input data and not the script itself.

    One of my guessing is the read fasta file, which, according to the READ ME file, has to contain collapsed reads with modified read_ID (>t0000001 15, >t0000002 45, and so on). My file does not follow exactly this example (mine is >rr1 15, >rr2 45, and so on) because I did not find a script to do that. Does any one know a script for doing the exactly same read_ID?

    Or does any one know what the problem might be, if not this one?

    I would appreciate any feedback.

    Kind regards,

    Vinicius

  • #2
    I have problem with mireap's mapping file. In mireap, i do not understand -m (map.txt) option. mireap is using for novel mirna prediction. I am not able to understand which software generate this file(map.txt). I do not understand the format of file.Can you please explain.

    Comment


    • #3
      I know the question is very old, but still want to reply for future users.

      You need to generate the map.txt file by mapping ur microRNA reads to ur genome or transcriptome using bowtie or some other tool.

      I did mapping using mapper.pl script from mirdeep2 software module.

      Comment

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