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?
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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