nCount and nFeature

[DHelix]

Hi, I'm wondering if anyone could explain what the nCount and nFeature in the metadata represent.
Thanks!

[timoast]

nCount is the number of total counts for that cell
nFeature is the number of features with >0 counts in the cell

[timoast]

please see answer above

[DHelix]

Hi @timoast,
Yes, I have read your answer above but I am still not clear what the nCount and nFeature exactly are.
Does the "total counts" mean "total fragments"?
And what exactly is a feature? Does it mean "a peak"?
And why are nCount and nFeature highly correlated?
BTW, I'm working with scATAC-Seq data, generated using 10X Genomics scATAC platform.
Thanks for your time!

[DHelix]

I used CountFragments() to calculate the total fragments per cell and the numbers are different from nCounts (their correlation is ~ 0.7). Now I don't think the nCount represents the number of fragments in each cell.
The nCounts values are generally smaller than the numbers of total fragments, so it doesn't sound like reads or Tn5 cutsites either.
So what is the "total counts" in your answer? Thanks!

[timoast]

Total counts is the total counts for the cell in the count matrix that you provide (the column sums of the matrix). Total fragments is the total number of sequenced DNA fragments for the cell, which could include fragments that are not quantified in the count matrix (falling outside of peaks)

[DHelix]

Hi @timoast, I see. Thank you so much for taking the time to answer my questions!