I've seen a lot of references to removing rRNA with bbduk.sh but I haven't seen specific commands that should be used. Is there a recommended parameter setting that could be used? Would this change with respect to read length?
My plan was to do the following:
- kneaddata to run trimmomatic and remove human contamination
- bbduk.sh to bin out rRNA (might do something w/ this later)
- rnaspades.py to assemble the transcripts
I'm very familiar with steps 1 and 3 but I haven't experimented much with bbduk.sh. I'm very impressed with the rest of the bbsuite so I'm looking forward to adding this into the pipeline.