pslReps

We use the following pslReps parameters:

RefSeq mRNA -minCover=0.15 -minAli=0.96 -nearTop=0.001

mRNA in same species: -minAli=0.96 -nearTop=0.005

mRNA in different species: -minAli=0.25

ESTs in same species: -minAli=0.96 -nearTop=0.005

ESTs in different species: -minAli=0.10

 

When pslReps can't find a significant difference between two places to map an cDNA, or when due to assembly errors or cDNA chimerism different parts map to different places, it will leave multiple lines in the output even under very stringent parameters.