I am running RASQUAL on scATAC-seq data from 172 individuals and noticed that the fSNP are never present in the output. No matter how I adjust filters (for both fSNP and rSNP), the SNPs within the ATAC peak are never included in the output. How can I ensure that SNPs with the ATAC are tested? I have poured over the documentation and past tickets and cannot seem to find an answer.
I am running RASQUAL on scATAC-seq data from 172 individuals and noticed that the fSNP are never present in the output. No matter how I adjust filters (for both fSNP and rSNP), the SNPs within the ATAC peak are never included in the output. How can I ensure that SNPs with the ATAC are tested? I have poured over the documentation and past tickets and cannot seem to find an answer.