Hi everyone!
I am analyzing sc ATAC-seq data with Signal tool integrated with Seurat. I only have the peak matrix and the fragment file. The metadata from cellranger has not been provided to me. To perform the quality control step I filtered the samples by the nucleosomal signal, TSS enrichment score and blacklist ratio. However I want to annotate in the metadata the total number of fragments in peak and the fraction of fragments in peaks. I have tried the last one with the FRiP function but the results of this is very low ( the highest values in only 1.4%).
Does anyone know how I can get these metrics correctly without the metadata?
I also want to to ask what is the nCount_peak and nFeature_peak that appear by default in the atac metadata and how they differ.
Could it be that nFeature_peak is the count of fragments in peaks and I can get the percentage of fragment in peak from it?
Thank very much in advance and sorry for my English!
