Hello! This is my first post and I don't think that there is a post already dealing with my problem 
My project is to perform de novo assembly on RNA-seq data. The sequencing protocol used is Ion Torrent Proton and I was wondering if someone had an idea of all the biases that I should take care of. In particular, what are the mismatch or repeat sequencing biases, and are there different qualities between the body and the ends of the RNAs? I'll use Trinity (I still don't know if I'll use it via Galaxy or directly) as the assembly program
Thanks for your answer!
Thibault
My project is to perform de novo assembly on RNA-seq data. The sequencing protocol used is Ion Torrent Proton and I was wondering if someone had an idea of all the biases that I should take care of. In particular, what are the mismatch or repeat sequencing biases, and are there different qualities between the body and the ends of the RNAs? I'll use Trinity (I still don't know if I'll use it via Galaxy or directly) as the assembly program
Thanks for your answer!
Thibault