<p>I am working on a RNA-Seq data. The Fastqc shows that data has duplication level of &gt;65%. Can anyone tell me how I can extract the duplicated reads and quantify them? I am also interested to rank those duplicated reads.</p>

<p>Thanks!</p>

<p>After marking duplicates (with your favorite program) you can use the <a href='http://samtools.sourceforge.net/'>samtools</a> flag to pull out the reads you want.</p>

<p>Just set the include flag:  <a href='http://samtools.sourceforge.net/'>samtools</a> view -f 0x400:</p>

<p>0x400 PCR or optical duplicate</p>
