Question: Compare the DNA footprinting between different samples when using ATACseqQC
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gravatar for aimin.at.work
11 months ago by
aimin.at.work0 wrote:

I am using ATACseqQC to plot DNA footprinting.  I want to compare the DNA footprinting between different samples.  Would it be possible to get  DNA footprinting graphs with same scale to make them be comparable? For example, for CTCF, I got some from 0 to 0.2, other from 0 to 0.14, from 0 to 0.25, etc. Also, what is the meaning of the 2 discontinuous red lines?

Thanks in advance

Aimin

atacseqqc • 214 views
ADD COMMENTlink modified 11 months ago by Ou, Jianhong1.1k • written 11 months ago by aimin.at.work0
Answer: Compare the DNA footprinting between different samples when using ATACseqQC
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gravatar for Ou, Jianhong
11 months ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi Aimin,

Now, in the next development version, you can control ylim. I add this possibility today. You can try it by

library(devtools); install_github("jianhong/ATACseqQC")

The dot red lines is the fragmentation fit line of the signals.

If you want to compare footprinting between different samples, you may want to sample the bam files into same level and then to compare.

Jianhong 

ADD COMMENTlink written 11 months ago by Ou, Jianhong1.1k

Thank you,

what does the fragmentation fit line of the signals indicates?

Aimin

 

ADD REPLYlink written 11 months ago by aimin.at.work0

The fit line indicates distal cut-site probability, proximal cut-site probability and the TF avoidance cut-site probability. The difference between  proximal cut-site probability and the TF avoidance cut-site probability indicates the avoidance of the TFs. And the difference between distal cut-site probability and proximal cut-site probability indicates the enrichment of the cut-site nearby the TFs.

ADD REPLYlink written 11 months ago by Ou, Jianhong1.1k
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