quality filtered illumina PE reads

[Wallysb01]

Hi all,

So I have illumina data in the standard phred 33 format with each pair separated into different files. What would be the best way to run a quality filtering script and retain the paired information?

I'm worried, maybe irrationally, that if filter each pair file individually that the resulting files will no longer contained paired information as one end get filtered out on one side, but not on the other.

Any particular suggestions?

[maubp]

I'm worried, maybe irrationally, that if filter each pair file individually that the resulting files will no longer contained paired information as one end get filtered out on one side, but not on the other

You should worry - that can and does happen if the forward and reverse files are filtered separately. Tools that look at the read names (like MIRA) won't care, but this makes preparing the input for say Velvet tricky.