Hi everyone, I am quite new to the ChIP-seq business and wetlab scientist so sorry for the maybe stupid question. I analyse epigenetic changes during the differentiation from cell type A to cell type B and performed Chip-seq of two different marks (X and Y). I used SCIER + Diffbind to identified differential enriched regions for both marks in the two conditions. I noticed that loci which gain X loss Y during the differentiation from A to B and vice versa. But loci which loss X dont show any correlation with Y and vice versa. By using ngs.plot I was able to visualize this impression by plotting the Chip-seq signal of X and Y from celltype A and B over regions which for example gain X. There you see an increase of ChIP-seq signal of X in A compare to B (as expected) and a loss of Y in the same loci (as it was my impression). However I would like to put some numbers in this but not sure how. Maybe the most simple way is just to compare the readcounts of X and Y of these loci using for example DESeq2. However X and Y are Chip-seq under the same conditions but with total different antibodies and so one. So not sure if I can then simply compare or I need addtional normalisations (input controls ???). Is there a dedicated tool to do such analysis?
Thanks a lot, Flo