<p>Hi All,</p>

<p>Again on the issue of marking duplicates...</p>

<p>If you have single end reads tools like Picard MarkDuplicates mark as duplicates reads sharing the same 5&#39;end coordinates and ignore the 3&#39; coordinate (see <a href="http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-does-markduplicates-work">here</a>). Is this the right thing to do?</p>

<p>I can see the point in looking at only 5&#39; coordinates when the read length was quite a bit shorter then the fragment length (say 35-70 bp) and sequence quality dropped after ~50bp.</p>

<p>But now you can get reads up to 300bp, which is well into or above the range of the fragment length. So reads sharing the same 5&#39;end but different 3&#39;end might well be genuine independent fragments and MarkDuplicates would get them wrong. Am I missing something? Does anybody know of a tool that looks at both 5&#39; and 3&#39; ends for SE reads?</p>

<p>An update on this... I ended up writing a program to mark duplicates sharing start and end coordinates on the same strand and read group. The program is here <a href="https://github.com/dariober/Java-cafe/tree/master/MarkDupsByStartEnd">MarkDupsByStartEnd.jar</a> if anyone is interested.</p>

<p>@Kamil, I&#39;m afraid samtools rmdup also look for 5&#39;end only.</p>
