On 22 Feb 2014, at 20:55 , Gutierrez, Juan <Juan.Gutierrez@xxxxxxxxxxxx> wrote: > I am trying to do RNA-seq de novo on a polyploid (hexaploid) genome using a > combination of 454 and illumina 100bp paired ended reads. The three copies of > each gene are highly similar to one another. Care to expand a bit more on the “highly similar” criterion? Is it one diff per 100bp, per 1000bp, per 10000bp, …? B.