Hello! I am using the methylong pipeline for a few weeks now and I do not understnd how does the it handles barcodes in the pod5 file. I think it is quite common to have all your sequencing data mixed in the same files. But having different barcode corresponding to different experimental condition. Then if one want to make a differerential analysis study (with dmr pair for instance), one need to be able to specify to the program which barcode to select. What I want to do is that each barcode corresponds for instance to a different sample for instance. It is also needed to specify to dorado demux which barcode kit has been used. I do not understand how this is done in your pipeline.)

sample,group,path,ref,method,barcode
Project_23_24_DAM_S288c,DAM_S288c,pod5/,ref.fasta,ont,barcode23
Project_23_24_NoDAM_S288c,NoDAM_S288c,pod5/,ref.fasta,ont,barcode24

While I am not deeply familiar with the pipeline, I think it does not perform demultiplexing and you would need split your pod5 by barcode and then feed in the individual files as samples. Maybe I am wrong and @Yilia X can comment (@Jin Khoo is currently traveling)

Ok, then I am not sure I understand how you perform dmr step.

I am not maintaining this pipeline, and cannot answer your questions

Ok thanks

@Léo Tarbouriech Thank you for your question. Currently, methylong doesn't support demultiplexing. It's a tricky issue, and we're discussing and working on it.