Fixing mate pairs in fastq

[lukas1848]

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?

[kga1978]

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

[lukas1848]

thanks, that's exactly what I need.