John M. Gaspar

The paper compares short paired-end and long single-end RNA-seq reads, finding that short paired-end reads provide more accurate expression and differential expression results despite fewer total bases.

Running MACS2 in default single-end mode on paired-end ATAC-seq miscalculates fragment coverage and calls low-coverage peaks; a modified MACS2 adds peak-length and gap parameters and fixes calculation bugs.

The paper shows that MET-2/SETDB1 and its interactors LIN-65/ATF7IP and ARLE-14/ARL14EP regulate the timing of heterochromatin formation during C. elegans embryogenesis.