Extended Data Fig. 9: Sequencing depth impact loop detection but not compartmentalization.
From: Systematic evaluation of chromosome conformation capture assays
a. Spearman correlation of the eigenvectors for different sequencing depths in H1-hESC. Each point represents one sampled experiment. X-axis shows the sequencing depth (200 M reads-2B reads) and the y- axis shows the correlation of the eigenvectors for each depth with the eigenvector of the experiment with 2 Billion reads. The bottom plot shows the zoomed correlations. b. Compartment strength of A compartment for experiments with different read depths quantified in cis and trans for H1-hESC. c. Compartment strength of B compartment for experiments with different read depths quantified in cis and trans for H1-hESC. d. # of loops detected in experiments with different read depths in H1-hESC. e-f. Analysis that is shown in a-d repeated for experiments performed in HFFc6 cells.
