Thanks for the training yesterday! I particularly liked going through the result folder and how it is structured. In my current run I have problems with the contamination and checking for duplicates. In all my samples there are either no duplicates or 100% duplicates. The samples are coming from different experiments, so it is likely that barcodes have been reused. I thought in the Airrflow pipeline the

cell_id

would be changed to a unique

cell_id

by adding the

sample_id

in front. Is this not the case and do I have to manually do this? Samples are marked as duplicates if they are from the same

subject_id

, thus I am wondering if this was merged with the

cell_id

. I started the pipeline with already assembled cellranger files. Can I stop the pipeline to check for contamination? I found the pararmeter

--detect_contamination

, but I think this one only works with bulk data?