Question: Peak center for ATAC-seq data
1
gravatar for christacaggiano
2.1 years ago by
UCSF
christacaggiano20 wrote:

I am creating a coverage plot +/- 250bp around a transcription start site with various ATAC-seq replicates. I have created these plots very easily for S2 (drosophila embryonic) cells using microarray data. However, I am having a hard time locating precise peak centers in the ATAC data which is very noisy. Ideally, I would like a smooth curve centered at 0bp. Right now, my plots seem to be really skewed right or left depending on the replicate (I am actually finding the peak centers by hand, using a BW visualization file which is clearly not working nor is that efficient) Is there any better, consistent, way of doing this? I am calling peaks using HOMER and creating the coverage plot using perl and python scripts.

ADD COMMENTlink modified 2.1 years ago by igor7.1k • written 2.1 years ago by christacaggiano20
1

If you call peaks using macs2, it also give the summit (--call-summit) , which is the peak center.

ADD REPLYlink modified 21 months ago • written 2.1 years ago by geek_y8.8k
1
gravatar for igor
2.1 years ago by
igor7.1k
United States
igor7.1k wrote:

This sounds like two separate questions. Do you want to make TSS enrichment plots or find peak centers?

To visualize enrichment at TSS, you can try these methods:

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by igor7.1k

can i use chIp seeker for ATAC seq data?

ADD REPLYlink written 17 months ago by krushnach80440
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