m6A Peak Calling

exomePeak2 (Recommended)

library(exomePeak2)

Peak calling with biological replicates

result <- exomePeak2( bam_ip = c('IP_rep1.bam', 'IP_rep2.bam'), bam_input = c('Input_rep1.bam', 'Input_rep2.bam'), gff = 'genes.gtf', genome = 'hg38', paired_end = TRUE )

Export peaks

exportResults(result, format = 'BED')

MACS3 Alternative

Call peaks treating input as control

macs3 callpeak
-t IP_rep1.bam IP_rep2.bam
-c Input_rep1.bam Input_rep2.bam
-f BAMPE
-g hs
-n m6a_peaks
--nomodel
--extsize 150
-q 0.05

MeTPeak

library(MeTPeak)

GTF-aware peak calling

metpeak( IP_BAM = c('IP_rep1.bam', 'IP_rep2.bam'), INPUT_BAM = c('Input_rep1.bam', 'Input_rep2.bam'), GENE_ANNO_GTF = 'genes.gtf', OUTPUT_DIR = 'metpeak_output' )

Peak Filtering

Filter by fold enrichment and q-value

FC > 2, q < 0.05 typical thresholds

awk '$7 > 2 && $9 < 0.05' peaks.xls > filtered_peaks.bed

Related Skills

• merip-preprocessing - Prepare data for peak calling

• m6a-differential - Compare peaks between conditions

• chip-seq/peak-calling - Similar concepts