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Old 06-30-2009, 06:07 AM   #1
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default illumina de novo txome assm: overlapping paired ends or long inserts?

There seems to be some debate about the optimal paired-end read length for de novo transcriptome assembly.

Some are advocating selecting for short fragments - so short you can see overlap between pair mates. Others contend there should be bigger inserts between the ends in order to build the scaffold and leverage pairing information.

I would like to hear your views on this.
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Old 10-15-2009, 04:46 AM   #2
MattB
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Location: Norway

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Hi Zigster,

Interesting question you pose, we have had some paired-end transcriptome sequencing done and for some reason have quite a small average insert size (ie. lots of overlap between pair mates). It's hard to say what impact this has had on contig/scaffold building, since we haven't got anything to compare to! Like you, I would be interested to hear what others have observed, as it might influence our strategy for futher transcriptome sequencing that we plan to do.

Matt
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