Do Too few Median fraction of fragments overlapping peaks lead to few features?

[jiangpuxuan]

The Median fraction of fragments overlapping peaks of my dataset is 1.421%. When I ran to getMarkerFeatures() or getMarkers(), the cell clusters in my dataset turned to have too few markers or marker peaks..... ( only 7 markerpeaks in all 4 cell clusters, FDR<0.05, log2FC>1)
I would like to figure out whether it is caused by my poor Median fraction of fragments overlapping peaks .
Thank you for your help!

Here is my archR project:

class: ArchRProject 
outputDirectory: /Array-Tuqiang/pxjiang/analysis/atac/CRC_P07A/proj_crc07_hg19 
samples(1): Human_0721
sampleColData names(1): ArrowFiles
cellColData names(34): Sample TSSEnrichment ... ReadsInPeaks FRIP
numberOfCells(1): 1364
medianTSS(1): 6.142
medianFrags(1): 3717

[rcorces]

Something does not seem right here. The fraction of fragments overlapping peaks is far too low.

[jiangpuxuan]

Something does not seem right here. The fraction of fragments overlapping peaks is far too low.

Sorry, does it mean that my dataset cannot be used in downstream analysis?

[huangmiao1996]

Hey, I also encountered the question. Could we talk together for further investigation in Wechat? If so, you could contact with me by email [email protected].