search

bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
109 stars 21 forks source link

Your paper circle plot #26

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi , Sorry for this silly question, but I was wondering how you made that circle plot in your paper. As you mentioned in the paper you binned genome in 1mb regions, did you also binned methylation frequency file and mean/sum methylation frequencies in those 1mb regions?

I am trying to reproduce a similar plot but mine is completely different. Thanks, Vahid.

PengNi commented 4 years ago

Hi @vahidAK ,

In my circos plot, I just use the number of CpGs (which deepsignal can detect but BS cannot detect, coverage>=5) in each binned region to plot a histogram. I didn't use the methylation frequency file. The plot is to show that using nanopore reads can detect more CpGs than bisulfite sequencing.

Best, Peng