Adapt trimmomatic command

[larahurban]

Dear team,

May I suggest changing the trimmomatic command in this tutorial so that it firstly lists the ILLUMINACLIP command and then the further processing of the read including the sliding window approach? I think it makes more sense to firstly cut the adapter before removing parts of the sequence and consequently potentially removing part of the adapter - which would make the processor recognising adapters even more difficult.

Please let me know your thoughts, or if there is a reason to keep this command like it is.

Thank you,
Lara