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Old 04-04-2013, 07:15 AM   #1
deepbiomed
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Location: Danbury, CT

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Default 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 ?

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Deep
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Old 04-04-2013, 08:04 AM   #2
davidblaney
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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.
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Old 04-04-2013, 08:08 AM   #3
maubp
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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.
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Old 04-04-2013, 08:14 AM   #4
maubp
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See also this BioStars post which is a duplicate of this thread: http://www.biostars.org/p/68239/
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