r2ascension/skill_repo/bio-epitranscriptomics-m6a-peak-calling

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')

# 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

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'
)

# 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