Hi Ryan,
I have a bunch of reads after sequencing my library on MinION, prepared using only two adapters that are included in the SQK-LSK108 ligation sequencing kit from Oxford Nanopore. The simplest case really. I replaced existing non-barcode adapters with the two Y-adapters according to the note by ONP. But when I tried commenting out the barcodes in the ADAPTERS list (adapters.py file), the program threw an error saying that the barcodes string cannot be empty (source code string cannot contain null bytes). Through trial and error I found out that I can only exclude the native barcodes set - but keep at least one of them intact - for the program to proceed without error. Not knowing anything about python syntax and being short of time I couldn't find a nicer fix. The problem got worse because I had to lower the adapter threshold and suddenly the program started finding barcode adapters in my reads (or so it seemed according to the report in my terminal).
Would you consider making barcodes search optional? And why include all the available adapters in the set? If I know that most of them are simply not there in the first place, some of them probably no longer manufactured, why waste CPU time or worse trim parts of the reads that align to adapters by pure chance?
Hi Ryan, I have a bunch of reads after sequencing my library on MinION, prepared using only two adapters that are included in the SQK-LSK108 ligation sequencing kit from Oxford Nanopore. The simplest case really. I replaced existing non-barcode adapters with the two Y-adapters according to the note by ONP. But when I tried commenting out the barcodes in the ADAPTERS list (adapters.py file), the program threw an error saying that the barcodes string cannot be empty (source code string cannot contain null bytes). Through trial and error I found out that I can only exclude the native barcodes set - but keep at least one of them intact - for the program to proceed without error. Not knowing anything about python syntax and being short of time I couldn't find a nicer fix. The problem got worse because I had to lower the adapter threshold and suddenly the program started finding barcode adapters in my reads (or so it seemed according to the report in my terminal). Would you consider making barcodes search optional? And why include all the available adapters in the set? If I know that most of them are simply not there in the first place, some of them probably no longer manufactured, why waste CPU time or worse trim parts of the reads that align to adapters by pure chance?