Run MACS2 combining replicates.
You don’t need to use “samtools merge”, just
$ macs2 callpeak -t H3K36me1_EE_rep1.bam H3K36me1_EE_rep2.bam -c Input_EE_rep1.bam Input_EE_rep2.bam -B --nomodel --extsize 147 --SPMR -g ce -n H3K36me1_EE
https://github.com/macs3-project/MACS/wiki/Build-Signal-Track#Fix_the_bedGraph_and_convert_them_to_bigWig_files
for j in DM GM
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{j}_MyoD*.bam|sed 's/_MyoD_ChIPseq_Rep[0-9]_trimmed.bam//g' |sort -u |while read id;do samtools merge ./mergeBam/
jMyoD∗.bam∣sed′s/MyoDChIPseqRep[0−9]trimmed.bam//g′∣sort−u∣whilereadid;dosamtoolsmerge./mergeBam/id.merge.bam $id.bam ;done
done
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