Using fastx_trimmer with paired reads

[vgaout]

Hi to all!

I am trying to replicate some results from an article and here the authors claim that they use fastx_quality_filter + fast_trimmer with paired end reads. I am not sure how to do this. I mean, it seems that there is not an option to use this programs in two paired reads at the same time. In case that I use it for every read independently, I supose that I have to sincronize again the reads. Is this correct?

Thank you,
Vera