ATAC-Seq and featureCounts
0
0
Entering edit mode
3 months ago
qudrat.nii ▴ 10

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?

ATAC-Seq featureCounts • 605 views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

I use following command:

featureCounts - p -a peak.saf -F SAF -o readCountInPeaks.txt ${sample}.bam
ADD REPLY
1
Entering edit mode

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

--countReadPairs 
ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

ADD REPLY

Login before adding your answer.

Traffic: 2498 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6