Called peaks for 8 D. melanogaster functional genomics data sets

Analyses were performed on chromatin accessibility (ATAC-seq, DNase-seq, FAIRE-seq), histone modification ChIP-seq (H3K4me1, H3K4me3, and H3K27ac), and direct enhancer activity reporter via an ectopic plasmid based assay (STARR-seq) data sets generated from experiments in D. melanogaster. The ATAC-seq and FAIRE-seq data sets were generated using wandering third instar larvae eye antennal imaginal disc tissue extracted from the FRT82 stock (Davie et al., 2015), while all other data sets were generated from Drosophila melanogaster S2 cells (Arnold et al., 2013; Henriques et al., 2018; de Almeida et al., 2022). Sequencing reads were downloaded from the NIH SRA, cleaned and trimmed using Trimmomatic v0.39 (Bolger et al., 2014), and aligned to the D. melanogaster r6.45 genome (Hoskins et al., 2015) using BWA (bwa aln, default settings) v0.7.17-r1188 (Li and Durbin, 2009). The D. melanogaster genome was downloaded from Fly Base (Gramates et al., 2022). Aligned reads were filtered for mapping quality (-q 10 -F 0x0200 -F 0x0100 -F 0x004) using SAMTools v1.11 (using htslib v1.11-4) (Li et al., 2009). Peaks were called using MACS2 v 2.2.7.1 (Zhang et al., 2008) with FDR correction (-q 0.01) and the preset D. melanogaster genome size (-g dm). The data sets varied in terms of read lengths, single-end or paired-end, and the availability of control data, so parameters were adjusted appropriately. MACS peak calling parameters for ATAC-seq and FAIRE-seq data were taken from Davie et al. (2015).