Hidden epigenetic mechanisms behind chronic UTIs found NatureMicrobiol
). The promoter was defined as 1 kb upstream of transcription start site. Genomic annotation priority was assigned in the following order: promoter, coding exon, 5’ UTR, 3’ UTR, intron and intergenic. DMRs were assigned to annotation if the DMR overlapped 20% of the annotation using BEDTools v2.27.
A detailed list of commands and parameters can be found under Code availability. Briefly, fastqQC v0.11.9 was used to assess the read quality. Subsequently, the paired-end reads were trimmed with Cutadapt v1.9 and reassessed using fastqQC. Reads were then aligned using bowtie2 v2.3.4.1. Mitochondrial reads were removed using samtools v1.9 and deduplicated using Picard v2.8.1 MarkDuplicates. Uniquely mapped reads were extracted using samtools view. Peaks were called using MACS2 v2.1.1.
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