<p>Hi all,
here are some questions about <strong>paired-end sequencing</strong> for NGS:</p>

<ul>
<li>What are the main differences between <strong>mate-paired</strong> sequencing and <strong>paired-end</strong> sequencing; Should I care when I use tools like 'samtools', maq, etc.... ? Should one, and only one short read, should be paired with another one (1-1)?</li>
<li>What is <strong>removing duplicates</strong> ? does it mean that a <strong>pair</strong> of short reads has been mapped at two distint positions on the genome or does it mean that a pair matched too many time at one position ?</li>
<li>Knowing that <strong>bwa sampe</strong>  "Generates alignments in the <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a> format given paired-end reads. Repetitive  read pairs will be placed randomly", is there any need to "remove the duplicates" ?</li>
<li>How does picard <strong>MarkDuplicates</strong> work ? How can I find the reads that have been 'tagged' ? will it remove the reads from the <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file ?</li>
</ul>

<p>Thanks</p>

<p>Pierre</p>

<p>paired-ends and mate pairs are different protocols. The distance between mate pairs are much longer (2-5kb), while paired-end fragments are rarely more than 500bp apart and can even have <em>negative</em> distance (overlapping pairs)</p>
