Parameters for RNA004 processing

Hi, 
I'd like to use readuntil on RNA004 data but I didn't find the parameters for trimming polyA tail, so I used the same for RNA002. It worked well on filtering mtRNA but the accuracy of recognizing mRNA (0.86) is lower than you mentioned in the paper. I wonder if I used the wrong paramters or classified biotypes in wrong way, how did you do that? 