先对单个文件做了peak call，

/home/data/t210424/m6a/filtered/singlepeakcall.sh

#!/bin/bash

input_dir="/home/data/t210424/m6a/filtered"

output_dir="/home/data/t210424/m6a/peak2"

mkdir -p $output_dir

# 对每个样本进行peak calling

for file in $input_dir/*.bam; do

    base=$(basename $file .bam)

    sample=${base%%_*}

    replicate=${base#*_}

    # 运行MACS2进行peak calling

    macs2 callpeak -t $file -f BAM -n ${sample}_${replicate} -g hs -q 0.01 --nomodel --shift -100 --extsize 147 --keep-dup all --outdir $output_dir

done

然后在/home/data/t210424/m6a/peak2做overlap 脚本没写明白

bedtools intersect -a /home/data/t210424/m6a/peak2/RIP_sh_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/RIP_sh_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/RIP_sh_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/RIP_sh_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/In_sh_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/In_sh_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/In_sh_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/In_sh_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/In_Sham_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/In_Sham_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/In_Sham_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/In_Sham_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/In_SNI_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/In_SNI_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/In_SNI_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/In_SNI_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/RIP_sh_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/RIP_sh_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/RIP_sh_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/RIP_sh_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/RIP_Sham_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/RIP_Sham_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/RIP_Sham_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/RIP_Sham_common_peaks.narrowPeak && \

bedtools intersect -a /home/data/t210424/m6a/peak2/RIP_SNI_1.filtered_peaks.narrowPeak -b /home/data/t210424/m6a/peak2/RIP_SNI_2.filtered_peaks.narrowPeak -wa | bedtools intersect -a stdin -b /home/data/t210424/m6a/peak2/RIP_SNI_3.filtered_peaks.narrowPeak -wa > /home/data/t210424/m6a/peak2overlap/RIP_SNI_common_peaks.narrowPeak