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...



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
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