Salmon -- prepare reads

Question

[afabian]

Hi there

I use salmon for paired end data. I did already prepare the reads by standard quality trimming and adaptor clipping. I use trimmomatic for this. As it happens with my data, after this quality filter I lose many reads because one of the reads in the pair is not passing the filter.

Therefore I wondered how salmon deals with this kind of data. I actually did not find any recommendation that adaptor clipping should be done in the first place. What is you take on this? Does someone has any experience if the raw read or the cleaned read are advised to use together with salmon? As I understand the method it should be rather robust against adaptor contaminations.

thanks in advance.