Hello,
I am studying a mutation in the gene Spi1 versus the wildtype. We generated ATACseq and RNAseq, and saw a clear correlation between both (x = FC ATAC, y = FC RNA expression). In this post I represented the comparison between Homozygote and wildtype for my mutation.
I ran seacr to call peaks in Cut&Tag in stringent mode for different histone marks (H3K27ac; H3K27me3, H3K4me1) and my gene of interest Spi1. I would like to cross those data with ATACseq that we generated previously.
One idea would be to look at the regions differently open in ATACseq between mouse of different genotypes, and then look in those regions the normalized level of reads in each genotype. Does this idea make sense ? Or should I reason more in terms of differential binding for each marks and then cross those genomic regions ? What would be a good idea to integrate all those data ? Any examples or link to article ?
I have included on the graphe the differential binding at the peak of ATACseq position of my gene of interest SPI1 but I'm unsure for the next steps... Any help is really appreciated...