Question: Trimming And Thinning Of Paired-End Reads
0
Alicia R. Pérez-Porro • 20 wrote:
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/