two replicates and the combined have different signal
HYan-lei opened this issue · comments
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
![atac](https://private-user-images.githubusercontent.com/61328198/263782922-3fa44a51-07b6-463d-bd0f-fb5170fc3a60.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.5tEVW1OURUfCx4AgJLv0X6VcAlSfENnl_tHkGEsnBik)