ATAC-Seq and featureCounts

Question

[qudrat.nii]

Hello,

I have ATAC-Seq bam files and I want to know the quality of files, so I run featureCounts. I found the following result...

Successfully assigned alignments : 54255620 (40.3%)

Is it OK or what should be the percentage of assigned alignment?

[ATpoint]

If this is the percentage of reads overlapping callable peaks then this actually pretty good. Some context on commands and what you use as annotations here to count would be helpful though.

[qudrat.nii]

I use following command:

featureCounts - p -a peak.saf -F SAF -o readCountInPeaks.txt ${sample}.bam

[GenoMax]

If you are using -p for paired end reads then you will want to use following as well to count fragments.

--countReadPairs 

[ATpoint]

As said, if this is reads in peaks (FRiPs) then this is fine.

[seidel]

Sort of impossible to answer without more specific information. What organism? What annotation? Has anyone ever done ATAC Seq in this organism before? Do you have a positive control experiment (even in another organism to control for your analysis pipeline) that you can compare the number to?