I have noticed during quality control of my atac-seq data that one of my samples, sample #4, has an abnormally low number of fragments in ArchR but not in Signac. Is there a difference between how ArchR and Signac calculates the number of fragments for each sample? How does Signac calculate this value?
Hi,
I have noticed during quality control of my atac-seq data that one of my samples, sample #4, has an abnormally low number of fragments in ArchR but not in Signac. Is there a difference between how ArchR and Signac calculates the number of fragments for each sample? How does Signac calculate this value?
The ATAC_Fragments information came from the cellranger-arc count pipeline, which I added in as metadata. https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/per_barcode_metrics
Both ATAC_Fragments (Signac) and nFrags (ArchR) should represent unique nuclear fragments.
Signac:
VlnPlot(object = comb, features = c('ATAC_Fragments'), group.by = 'orig.ident',pt.size = 0,ncol=2, log=T)
ArchR: