Hi jsh58,
I have used Genrich to call peaks in my ATAC-seq data in two replicates separately and got a very different number of peaks in two replicates (~100 in one and ~27k in another).
I am trying to understand why there is such a huge difference. While using both the replicates together I get 48k peaks which is surprising and hard to infer. Please if you could help me understand why there is such a big difference while calling peaks separately. I understand that there might be a sample issue with one replicate but when I call peaks together I get more peaks which is difficult to understand.
Also, my second question is (see the attached snapshots of igv with two replicates)
I get two peaks (0,1) in one replicate but in the same position, only one peak is called in another replicate.
I am trying to understand when Genrich decides to merge the two adjacent peaks.
Another screenshot attached below:
In this why the peaks are not called in one replicate as we can see a good pileup.
Please help me understand the Genrich.
Thanks for the help.
Hi jsh58, I have used Genrich to call peaks in my ATAC-seq data in two replicates separately and got a very different number of peaks in two replicates (~100 in one and ~27k in another). I am trying to understand why there is such a huge difference. While using both the replicates together I get 48k peaks which is surprising and hard to infer. Please if you could help me understand why there is such a big difference while calling peaks separately. I understand that there might be a sample issue with one replicate but when I call peaks together I get more peaks which is difficult to understand.
Also, my second question is (see the attached snapshots of igv with two replicates) I get two peaks (0,1) in one replicate but in the same position, only one peak is called in another replicate.
I am trying to understand when Genrich decides to merge the two adjacent peaks.
Another screenshot attached below:
In this why the peaks are not called in one replicate as we can see a good pileup.
Please help me understand the Genrich. Thanks for the help.