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  • Combine pairend reads into one file for SOPRA

    Hi there,

    Sorry for a pitifully newbie question.

    How can I combine two fasta files, read 1 and read2 from a Illumina pairend run into a single file as this:

    >seq1read1
    cagtgtcgaggaac...
    >seq1read2
    gatatagagatctac...
    >seq2read1
    cagtgtcgaggttt...
    >seq2read2
    gatatagagatcgta...

    I want to try SOPRA and it requires the format above as matepair read input.

    Thank you very much.

    Hiroki

  • #2
    Try either shuffleSequences_fastq.pl included with Velvet or this:

    ngcrawford.com is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, ngcrawford.com has it all. We hope you find what you are searching for!

    Comment


    • #3
      Hi themerlin,

      Thanx a lot.
      I will try it.

      Best,

      Hiroki

      Comment


      • #4
        If you want more options, try searching for interleaving, the resulting file is often called an interleaved FASTA (likewise with FASTQ), because you interleave the forward and reverse read files to combine them.

        Comment


        • #5
          Hi maubp,

          Thanks a lot

          Comment

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