Why we need two instead of one kinds of Linkers in ChiA-PET? I think one is enough for the analysis and by the way the reads from two kinds of Linkers seem useless.
Hi chenxiaoyu4,
The answer is 5 weeks after your post, but maybe it will be helpful for others.
The idea behind using two linkers is to estimate random interactions.
If you just use linker A and then do the mapping, you cannot know which interaction is real and which one is just a result of random ligation.
By using two linkers you can get a background distribution of random interactions, which you can using to estimate the real signal.
For example in this paper, they use the chimeric interactions frequency to select the significant interactions count.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6