I have 3 ATAC-seq conditions, with 2 replicates in each. I want to compare how similar they are to each other. I mapped with BWA and the output bam file was converted to bigwig format using bamcoverage, and normalising using RPKM.
I then used multibigwigsummary as following:
./multiBigwigSummary bins -b cellpop1_rep1 cellpop1_rep2 cellpop2_rep1 cellpop2_rep2 cellpop3_1 cellpop3_2 -out cell123.npz --binSize=100
The PCA plot of the resultant count summary looks like this:
Am I right in thinking that my replicates cluster well together, meaning they are quite similar. However, there are differences in PC2. But the eigenvalues of this second component are minimal? Meaning that the differences are small between the samples, but they do exist?