Hi galaxy users,<div><br></div><div>I&#39;ve been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads.</div><div><br></div><div>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?</div>
<div><br></div><div>- 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?</div>
<div><br></div><div>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... </div>
<div><br></div><div>Thanks,</div><div>Alicia.<br clear="all"><div><div><br></div><div><br></div><div>––</div><div><br></div>Alicia R. Pérez-Porro<br>PhD student<div><br></div><div>Giribet lab</div><div>Department of Organismic and Evolutionary Biology</div>
<div>MCZ labs</div><div>Harvard University</div><div>26 Oxford St, Cambridge MA 02138</div><div>phone: +1 617-496-5308</div><div>fax: +1 617-495-5667</div><div><a href="http://www.oeb.harvard.edu/faculty/giribet/" target="_blank">www.oeb.harvard.edu/faculty/giribet/</a></div>
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