two replicates and the combined have different signal

[HYan-lei]

Hi,

I have the replicates for the data. After running the atac-seq pipeline, i converted _r2_R1.trim.srt.nodup.no_chrM_MT.bam and .pooled.tagAlign.gz file to tdf file. But in the IGV, I found the replicates and the combined have different signal. Can anyone help me with this issue? Thanks.

Here is the script i use:
samtools index T265_DPF1_r2_R1.trim.srt.nodup.no_chrM_MT.bam
bamCoverage -b T265_DPF1_r2_R1.trim.srt.nodup.no_chrM_MT.bam --binSize 25 --normalizeUsing RPKM -o $dir2/T265_DPF1_r2.bw
bigWigToWig $dir2/T265_DPF1_r2.bw $dir3/T265_DPF1_r2.wig
igvtools toTDF $dir3/T265_DPF1_r2.wig $dir3/T265_DPF1_r2.tdf hg19

bedToBam -i <(zcat T265_DPF1.pooled.tagAlign.gz) -g $dir/hg19.sizes > T265_DPF1_combined.bam
samtools sort -T /data/leihaiyan/original_data/tmpdir/T265_DPF1.sorted -o T265_DPF1_combined.sorted.bam T265_DPF1_combined.bam
samtools index T265_DPF1_combined.sorted.bam
samtools reheader $dir1/T265_DPF1_r2_R1.trim.srt.nodup.no_chrM_MT.bam T265_DPF1_combined.sorted.bam > T265_DPF1.bam
samtools index T265_DPF1.bam
bamCoverage -b T265_DPF1.bam --binSize 25 --normalizeUsing RPKM -o $dir2/T265_DPF1.bw