Closed weishwu closed 11 months ago
That will not work and IMHO you don't need to.
If you'd like to do modified base calling, just do it separately for each of the run datasets. Afterwards you take the BAM files, align the complete dataset to your reference genome and then use modkit
for methylation counts or any other tool for SNP calling or any other task ..
Hi @sklages, thanks for your reply. I see your point for methylation counts. For SNP calling I use Clair3 which takes into account the model used for basecalling. I asked this on Clair3 github and the answer was simply that I could not combine the runs from different models.
I have some historical ONT runs that were basecalled with these models:
I'd like to concatenate them to achieve high depth for variant calling and methylation calling. I have fast5 files for them. Could I concatenate the fast5 files, convert to POD5, and then use Dorado to do modified basecalling with the latest model? Will there be any incompatibility issue between Dorado/model and the old chemistry?
Thanks.