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  • Split Large FASTQ file in small FASTQ files with user defined number of reads Windows

    Hi All,

    Is there anyway I can split large FASTQ files into small FASTQ files with defined number of reads under windows environment, I know there are multiple option for unix but did not find anything for windows ?

    best
    Deep

  • #2
    I have used windows Power Shell to manipulate big files on occasion, this is a crude way to get first and second 100 reads. Only really suitable for simple splitting.

    Code:
    
    PS> Get-Content input.fastq | where { $_.readcount -ge 1 -and $_.readcount -lt 401} | Out-File first100reads.fastq
    
    PS> Get-Content input.fastq | where { $_.readcount -ge 401 -and $_.readcount -lt 801} | Out-File second100reads.fastq
    Maybe reworking this will help you. Depends on how you want to split the fastq's. This is a bit like the head unix command.

    Comment


    • #3
      Can you program?

      You can use scripting languages like Perl, Python and Ruby on Windows - the BioPerl, Biopython or BioRuby libraries should make splitting a FASTQ file up quite easy.

      Comment


      • #4
        See also this BioStars post which is a duplicate of this thread: http://www.biostars.org/p/68239/

        Comment

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