Ümran Yaman

Hi @eduff Yes, still creates the temp files in /var/folders... not to the directory where the other output files are. Only some markdown files are in that folder. When it...

Thank you! It indeed makes sense to aggregate the hap1 and 2. I am still not sure about discarding ungrouped calls. Is there any reason modkit pileup including ungrouped ones,...

Thanks @ArtRand! I am considering downstream analyses. I will perform differential methylation analysis across multiple samples and identify genes associated with the trait using aggregated methylation. From there, I would...