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Old 05-03-2012, 07:28 AM   #1
lukas1848
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Location: Germany

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Default Fixing mate pairs in fastq

Hi again,

I have some raw fastq files directly from illumina and somehow the PE files are out of sync. I hence need a script to fix these files. So far I used a perl script by Konrad Paszkiewicz (fastq_pe_even.pl), but after CASAVA's read identifiers were updated, it doesn't work anymore.
So far, I wasn't able to change the script successfully.

(btw. I used trimmomatic to clean my raw reads and apparently it could handle the messed up fastq files. It didn't fix them in the end, though)

Could someone provide an up-to-date script for simply fixing PE fastq files?
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Old 05-03-2012, 10:38 AM   #2
kga1978
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Default

Have a look at this

http://seqanswers.com/forums/showthread.php?t=17974

I have been using this:

http://seqanswers.com/forums/attachm...8&d=1330350938
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Old 05-03-2012, 11:08 AM   #3
lukas1848
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thanks, that's exactly what I need.
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