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  • VNou
    Junior Member
    • May 2012
    • 10

    Velvet-Insert Size

    Hello i am trying to assembly Staphylococus from the pair end library that i found in this site:


    and 2 short jumping libraries find at




    I want to ask 2 questions:

    1)In the run of velvetg i have to provide the insert length. How can i find it?

    2)Do i have after shuffling the short jumping libraries to reverse them?

    Thank you a lot
  • cliffbeall
    Senior Member
    • Jan 2010
    • 144

    #2
    Originally posted by VNou View Post
    Hello i am trying to assembly Staphylococus from the pair end library that i found in this site:


    and 2 short jumping libraries find at




    I want to ask 2 questions:

    1)In the run of velvetg i have to provide the insert length. How can i find it?

    2)Do i have after shuffling the short jumping libraries to reverse them?

    Thank you a lot
    For the insert length, if you don't specify it velvet will calculate it automatically. Alternatively you might map some reads to a reference genome or some assembled contigs and calculate it yourself..

    To the second question, with the latest version, you no longer need to shuffle (use the -separate flag). If they are the Illumina-type mate pairs (from circularization) you do need to reverse complement the second read.

    Comment

    • VNou
      Junior Member
      • May 2012
      • 10

      #3
      I found this command:
      shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq

      This command first shuffles and the reversed the output of the shuffle or it reverses the second read and then it shuffles?

      Comment

      • cliffbeall
        Senior Member
        • Jan 2010
        • 144

        #4
        You only want to run reverse complement on the shortjump_2.fastq file. The command you have will reverse complement both reads.

        Also like I said, with the latest velvet you no longer need the shuffleSequences script.

        Comment

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