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

[deepbiomed]

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

[davidblaney]

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.

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.

[maubp]

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.

[maubp]

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