Weird pattern showing up in log2 FC plots

[Janay Fox]

Hi,

Sorry if this is too unrelated but I have been trying to search up a potential answer as to why I am finding this pattern in my log2FC plots and I am not finding anything! I have created an assembly using samples from 4 groups and then ran a DEG analysis on each pairwise combination of the 4 groups. Then, I looked at how DEGs that overlapped between two of the comparisons were correlated. I used a couple of different ways to do this but one of the ways was plotting a scatterplot of the log 2FC from one comparison vs the log2FC from the other comparison. My two potential suspicions are that maybe it has something to do with low gene counts or something of the sort since I have quite a lot of "genes" but still I filtered for low CPM in the DEG analysis. Or maybe it has something to do with the fact that the two comparisons I am comparing are Group 1 vs Group 2 and Group 3 vs Group 2. Any suggestions you have would be greatly appreciated!

Best,

Janay