The ftm parameter from BBduk, trims to a certain modulo (usually 5) . I understand that is the desired behaviour to trim reads that are 151bp long (in stead of expected 150). However I now noticed that the files I get from the seq provider are not raw raw anymore and I guess that already did some adapter removal (still waiting on confirmation of this) and are thus not all 150 (151) bp anymore. In this case if I run BBduk with ftm=5 I will also trim back reads that are 149bp to 145, right? (I do see a small peak appearing at 145bp in my fastQC length graph ).
I'm wondering what the advice would be in this specific case, run BBduk with ftm=5 and potentially loose OK bases or not use the ftm=5 at all? I assume there is no way to tell BBduk to only ftm when the read is longer than 150bp?