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  • easy way to assemble 50% of reads?

    Is there an easy way to separate a large fastq file of raw reads in half? I would imagine this should be pretty easy. I want to see how assembling half of my reads would do with some command... but I also have access to CLC and there doesn't seem to be a way to specify 50% of reads. This is a 70M+ 100 bp dataset.

  • #2
    Hi,

    Open the sequencelist switch to table view (5th icon below the sequences). Select a number of sequences and press "create sequencelist".

    best
    Patrick

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    • #3
      Use awk or grep or something to filter by the tile.

      Or use unix head to get the top half of the file.

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      • #4
        If you know how many lines are in your file you can use the split command

        $ wc -l file.fastq
        100 file.fastq

        $ split -l 50 file.fastq

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        • #5
          The head command in Linux also alllows you to extract a number of lines from the start of the file (or use the tail command for the end of the file), without splitting the whole file:

          In analogy to the above:

          $ wc -l file.fastq
          100 file.fastq

          $ head -n 50 file.fastq > halfAFile.fastq

          cheers

          Micha

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          • #6
            The head command in Linux also alllows you to extract a number of lines from the start of the file (or use the tail command for the end of the file)
            FWIW, there's also the split command:

            Code:
            split -n 2 file.fa file.split.fa. # for splitting a file into two
            But bear in mind that raw reads from NGS runs frequently have low-quality reads near the start and end of the file, so you'll get a bit of quality bias from choosing a specific half of the file.
            Last edited by gringer; 11-11-2013, 08:33 PM.

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