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  • need to deinterleave/split all fastq files within a directory

    I've been using this script in the link below for several years when I need to split PE reads into separate R1 and R2 files.

    deinterleave FASTQ files. GitHub Gist: instantly share code, notes, and snippets.


    Does anyone know of a way to do the same thing recursively to a whole folder? I have 200 RNAseq samples that all need to be split.

  • #2
    Maybe you could loop over each of the interleaved files and run the script? Something like:

    Code:
    for j in *fastq; do deinterleave_fastq.sh $j *options; done
    If you could tell me your directory structure and the command for how you normally run the program, I could be more specific.

    Cheers,

    Matt.

    Comment


    • #3
      Originally posted by neavemj View Post
      Maybe you could loop over each of the interleaved files and run the script? Something like:

      Code:
      for j in *fastq; do deinterleave_fastq.sh $j *options; done
      If you could tell me your directory structure and the command for how you normally run the program, I could be more specific.

      Cheers,

      Matt.
      Code:
      deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
      The directory structure is just a folder of interleaved fastq files *0001reads.fq, *0002reads.fq, etc.

      Comment


      • #4
        Hi lac302,

        Well, you could do something like this:

        Code:
        for j in *reads.fq; do deinterleave_fastq.sh < $j $(basename $j .fq).F.fq $(basename $j .fq).R.fq [compress]; done
        It's still a bit tricky to tell without seeing the full file name, or understanding completely how the program works, but I think this should do the job.

        Best,

        Matt.

        Comment

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