I am trying to run the Filter command and I am running through one issue: the Filter command calls the summarizer.py script, but summarizer.py always uses default values for --barcode-orientation and --r2-barcodes arguments, even if we feed the Filter command with the --r2-barcodes argument. So it seems that summarizer.py should call the Filter --r2-barcodes argument.
One more question about this. It seems that the --barcode-orientation argument in summarizer.py is used to define the orientation the barcodes have to be red. I guess this is to accommodate sequencing runs on the Novaseq (original option) or on the NextSeq (reverse_complement) option. However, the default values at the moment in summarizer.py is original for --barcode-orientation argument, but 737K-cratac-v1.reverse_complement.csv for --r2-barcodes arguments. And I would have expected that the original 737K-cratac-v1.txt file from 10X (and not its reverse complement) would be the one to use with the original option.
Also I guess that the --r2-barcodes file has to be a csv and not txt file right?
Hi Andre,
I am trying to run the Filter command and I am running through one issue: the Filter command calls the
summarizer.pyscript, butsummarizer.pyalways uses default values for--barcode-orientationand--r2-barcodesarguments, even if we feed the Filter command with the--r2-barcodesargument. So it seems that summarizer.py should call the Filter--r2-barcodesargument.One more question about this. It seems that the
--barcode-orientationargument insummarizer.pyis used to define the orientation the barcodes have to be red. I guess this is to accommodate sequencing runs on the Novaseq (originaloption) or on the NextSeq (reverse_complement) option. However, the default values at the moment insummarizer.pyisoriginalfor--barcode-orientationargument, but737K-cratac-v1.reverse_complement.csvfor--r2-barcodesarguments. And I would have expected that the original 737K-cratac-v1.txt file from 10X (and not its reverse complement) would be the one to use with theoriginaloption. Also I guess that the--r2-barcodesfile has to be a csv and not txt file right?Thanks a lot.