title: LFY_rep2
design: High quality raw reads from ATAC-seq (FASTQC v.0.11.5;38) for the two replicates of 48 hpf embryos injected with mRNA LFY were trimmed for adapter sequences using Skewer (v.0.2.1; 39). All libraries were sequenced on Illumina HiSeq 2500 platform and raw reads were mapped to the reference zebrafish genome (GRCz10/danRer10) using Bowtie2 (v.2.2.6) with parameters -X 2000 and --very-sensitive40. To avoid clonal artefacts, the duplicated mapped reads were removed using Samtools (v.1.9; 41). Mapped reads were filtered by the fragment size (120 bp) and mapping quality (10). To call for enriched regions, MACS2 (v.2.1.0; 42) was used with the parameters --nomodel, --keep-dup 1, --llocal 10000, --extsize 74, --shift 37 and -p 0.07. For the ATAC-seq analysis, the two replicates were processed independently. Then, we applied the Irreproducible Discovery Rate (IDR, v.2.0.4;43) to obtain a confident and reproducible set of peaks.