I am trying to use mogsa to analyze ATAC -seq and RNA-seq data on the same samples. In the vignette example, the data matrices are multiple microarray data. If I use ATAC-seq data, what should I use as input? I was thinking a count matrix for a set of consensus peaks across all samples. However, in order to map it to the RNA-seq data presumably we need nearest gene annotations for each peak? IN taht case we will have multiple peaks mapping to a single gene - is this going to be problematic for mogsa? Is this the correct way to handle this type of data?
Any help is much appreciated.