<div class="gmail_quote"><div>(thank you Adina for the thorough reply!)</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><div>
If you're focused on scaffolding and longer assemblies in general, maybe you want to prioritize the retention of your paired ends. If you're having trouble completing assemblies at all, you might try discarding more data at the cost of paired ends. </div>
</div></blockquote></div><div><br></div>One way to get some of the advantages of both is to try and sequence an overlapping paired-end library. For example, if you have a fragment size of 250bp and you sequence 2 x 150bp, then you end up with about half your reads overlapping (which can be joined into lovely ~250bp single end reads) and other half remaining as paired-end reads. I then use the SE reads for diginorm (sorted by longest first) and experiment/explore with those. If needed, I then consider incorporating the PE reads. Assembly algorithms tend to be happier with SE reads only, and the longer the better. PE reads can be useful for longer range information, but they make assembly more difficult.<br clear="all">
<div><br></div>-- <br><font face="tahoma, sans-serif" size="1"><i>--Dr Torsten Seemann<br>--Scientific Director : Victorian Bioinformatics Consortium, Monash University, AUSTRALIA</i></font><div><font face="tahoma, sans-serif"><i><font size="1">--Senior Researcher : VLSCI Life Sciences Computation Centre, Parkville, AUSTRALIA<br>
--<a href="http://www.bioinformatics.net.au/" target="_blank">http://www.bioinformatics.net.au/</a></font></i><br></font></div><div><br></div>