Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads. As fas as i know if i want to use FASTX-TOOLKIT i have to treat my data as single-end, trim the adapter of the forward reads first and then proceed with the reverse reads. And same thing for the filtering by quality. Right? - Can i combine forward/reverse reads in a unique file with the FASTQ joiner and then proceed with the trimming of the adapters and the filtering by quality? If i do that, am i going to be able to remove the adapters of both directions reads? Am i going to be able to keep the broken pairs? I was reading that there is another toolkit, NGS QC TOOLKIT that allows you to work with paired-end reads and keep the broken pairs after the trimming and thinning. Did anyone try it? I think that has no galaxy option... Thanks, Alicia. –– Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/