recently I noticed
trimmomatic wasn’t trimming the adapters. In this case are Nextera, so I specified “NexteraPE”. I know this is the default, but I tend to specify most of the options for clarity. The result was a successful run of
kneaddata, but the reads still had all the adapters.
I noticed that if some trimmomatic options are specified , the command generated by
kneaddata doesn’t contain the adaptors file, so as a consequence, there is no adapters’ trimming. The options I’m referring to are
--trimmomatic-options, one or both, when specified, generate a command that doesn’t contain the adapter file. Options
trimmomatic don’t seem to have this problem.
$ kneaddata --version kneaddata v0.10.0