The intervene venn diagram is misleading

[danli349]

I found that The intervene venn diagram is misleading. I use the peak summits file and narrowPeak file of the same sample to do intervene venn, All of the summits are in narrowPeaks:

intervene venn -i macs2_2/DoxCD31mKATEpos3_summits.bed \
macs2_2/DoxCD31mKATEpos3_peaks.narrowPeak \
--names summits,narrowPeak \
--bedtools-options f=1bp \
--title DoxCD31mKATEpos3 \
-o venn \
--figsize 12 12 \
--fontsize 14 \
--dpi 300 \
--project DoxCD31mKATEpos3

When A overlap with B: The left area label (no overlap area) is total of A subtract overlap The right area label (no overlap area) is total of B.

It is better to show right area label with total of B subtract overlap.

[asntech]

@danli349 this is because you're setting the -f and not -F, and also, you don't need to set --bedtools-options f=1bp since bedtools by default works as 1bp, not as a fraction of A or B. The description of the fraction of A/B args of bedtools intersect are below. So try without --bedtools-options f=1bp - it should work.

-f	Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-F	Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).

[danli349]

Yes. I tried without --bedtools-options f=1bp it works perfect. Thanks a lot.

[asntech]

Great!