I am preprocessing my data with BBDuk and have some doubts regarding adapter-trimming. I want to delete all the sequences of adapters and primers from both ends of my reads. When I run BBDuk with ktrim=r and then the result with ktrim=l, I do not obtain the same result (for example, the number of deleted bases in the final file) than if I run it first with ktrim=l and then ktrim=r.
I would like to know if I am doing something wrong, and which would be the best order to do that.
On the other hand, when I perform the quality trimming I do not add any flag indicating the quality encoding. According to FASTQC analysis, my reads are encoded in Sanger / Illumina 1.9. Does the BBDuk recognises this automatically?
Thank you all in advance.