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.
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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