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

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