meRIP-seq peak-calling

Peak calling for hg38 was performed using ExomePeak2 (Meng et al. 2014) with the following flags (paired_end=true, library_type=1st_strand, consistent_peak=TRUE, genome=“hg38,” peak_calling_mode=”full_tx”), and only consistently detected peaks with Padj < 0.05 were considered true positives. Each data set (comprising six biological replicates of input and IP) was analyzed individually and comparatively (SARS-CoV-2-infected vs. uninfected, and HCoV-OC43-infected vs. uninfected).

Peak calling for SARS-CoV-2 and HCoV-OC43 was performed on sampled BAM files using MACS2 (Zhang et al. 2008) with the following flags (-f BAMPE -g 30000 -q 0.05 -B –call-summits –keep-dup auto –nomodel –extsize 150).