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  • pbm13
    Junior Member
    • Jan 2013
    • 5

    shuffleSequences.pl script in velvet

    Hello,

    I am trying to run velvet with RNAseq data from Illumina. While it does not say it in the velvet manual (that I saw at least), I have seen on other forums that you are supposed to interleave your fastq files to input into velveth for paired end reads and there is apparently a script associated with velvet called shuffleSequences.pl.
    I would like to use this because I think that is part of some troubles I have been having getting velvet to run but I do not see this script in the velvet download tar file:
    1) Do I need to use this for paired end sequences for velvet?
    2) If yes, then where can I get this script?

    Thank you for any help!
  • eni
    Junior Member
    • Dec 2009
    • 7

    #2
    shuffleSequences.pl location

    When you install velvet, it puts the shuffleSequences.pl in the contrib folder.
    Copy the file to your local directory and you should be fine...
    Last edited by eni; 04-26-2013, 10:41 AM.

    Comment

    • mastal
      Senior Member
      • Mar 2009
      • 666

      #3
      shuffleSequences.pl script in velvet

      what version of velvet are you using?

      since version 1.2.06 you can use the flag -separate, and you don' t have to interleave the files.

      see the velvet mailing list archives:

      Comment

      • kaps
        Member
        • Jan 2015
        • 71

        #4
        Originally posted by eni View Post
        When you install velvet, it puts the shuffleSequences.pl in the contrib folder.
        Copy the file to your local directory and you should be fine...
        Hi, How do I locate the contrib folder for velvet?

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142

          #5
          Originally posted by kaps View Post
          Hi, How do I locate the contrib folder for velvet?
          Look through the source code you downloaded.

          Comment

          • mastal
            Senior Member
            • Mar 2009
            • 666

            #6
            velvet_1.2.10/contrib/shuffleSequences_fasta

            Comment

            • kaps
              Member
              • Jan 2015
              • 71

              #7
              Originally posted by mastal View Post
              velvet_1.2.10/contrib/shuffleSequences_fasta
              Ok. I have copied shuffleSequences_fastq.pl to my folder but when I run shuffling as; shuffleSequences_fastq.pl lib4_align.end1.fq lib4_align.end2.fq lib4_all_ends.fq.
              I get an error as;
              -bash: shuffleSequences_fastq.pl: command not found

              where is the problem?

              Comment

              • kaps
                Member
                • Jan 2015
                • 71

                #8
                Originally posted by mastal View Post
                what version of velvet are you using?

                since version 1.2.06 you can use the flag -separate, and you don' t have to interleave the files.

                see the velvet mailing list archives:

                http://listserver.ebi.ac.uk/pipermai...ay/001705.html
                Noted. this option is further supported here: http://thegenomefactory.blogspot.com...sequences.html.

                I will not use shuffleSequences.pl!

                Thanks

                Comment

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