Hi All,
I have a question regarding trimming of adapters in NGS data. I have previously analyzed RNAseq data using brtim (https://www.sciencedirect.com/science/article/pii/S0888754311001339) without using adapter sequence. I am now analyzing smallRNAseq data, and I am using adapter sequence as adapter.fa using BBduk.sh from BBmap tools. Could you please clarify under what circumstances one would need to provide/know adapter sequence and when it is not necessary? 
One case is where there is a kit/prep specific adapter that is being used. This may require special handling of the downstream data based on the instructions included in the kit.

If you had paired end reads with enough pairs having short inserts then you can detect them by doing this: `bbmerge.sh in1=r1.fq in2=r2.fq outa=adapters.fa`