Extracting duplex reads for multiplexed samples

[dpaudel-tb]

Since barcoding is still under development in darado, I was wondering what alternative approach would be a proper way to extract duplex reads for multiplexed samples? I am thinking along the lines of the following:

1. Multiplex using Guppy - to get read ids associated with each barcode
2. Extract sequences from duplex_orig.sam [step 3 of duplex-tools (Stereo basecall all the reads)] for reads that match the read ids associated with each barcode (from step 1 above)
   Can you please suggest?
   Thanks

[ollenordesjo]

Hi @dpaudel-tb, thanks for the question

Yes, I think that is one sensible approach you could use at the moment.

Ideally you'll have the same barcode classification for both template and complement read (if TP rate is high enough). You would have to decide whether you're ok with support from one of the reads, or whether you need barcode classification support for both reads. I think just looking at the template barcode classification might be easiest to start with.

[dpaudel-tb]

Thank you @ollenordesjo !