QC about TSS.enrichment and nucleosome_signal

[siqi-zZ]

Hello,

I have a question, I found our sample have low scATAC-seq library quality. can I change filter value?
like stander is
pbmc <- subset(
x = pbmc,
subset = nCount_peaks > 3000 &
nCount_peaks < 30000 &
pct_reads_in_peaks > 15 &
blacklist_ratio < 0.05 &
nucleosome_signal < 4 &
TSS.enrichment > 3
)
pbmc

can I change like this for got more fregments?
pbmc_donor1 <- subset(
x = pbmc_donor1,
subset = nCount_peaks > 3000 &
nCount_peaks < 50000 &
pct_reads_in_peaks > 15 &
blacklist_ratio < 0.05 &
nucleosome_signal < 1 & # nucleosome_signal < 4 &
TSS.enrichment > 1 # TSS.enrichment > 3
)
The attachement is my sample before QC.
Wati for respond and thinks for useful package!!!!

[timoast]

Yes, these thresholds are meant to be adjusted for each dataset. The information shown on the website is only a guide.

[siqi-zZ]

thank you so much!!