I have RNA-seq samples that are highly contaminated with Illumina PCR primer 2.01, which program is best to use to remove those?
<p>I&#39;d recommend bbduck from the <a href="http://sourceforge.net/projects/bbmap/">BBMap suite</a>. It has included a lot of adapters and primer sequences, is very fast, and you can trim next to adapters also low-quality tails. Additionally, it is keeping your paired-end data in the correct order (if one read is removed, the other is removed too).</p>
