Question

Compare the DNA footprinting between different samples when using ATACseqQC

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aimin.at.work ▴ 10

@aiminatwork-12324

Last seen 5.4 years ago

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 • 1.2k views

ADD COMMENT • link updated 6.3 years ago by Ou, Jianhong ★ 1.3k • written 6.3 years ago by aimin.at.work ▴ 10

score 0 · Answer 1 · 2018-07-23

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Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 9 hours ago

United States

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 COMMENT • link 6.3 years ago Ou, Jianhong ★ 1.3k

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Thank you,

what does the fragmentation fit line of the signals indicates?

Aimin

ADD REPLY • link 6.3 years ago aimin.at.work ▴ 10

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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 REPLY • link 6.3 years ago Ou, Jianhong ★ 1.3k