I have an old post describing some noisy ATAC-seq data. I went back and did some more diagnoses. However, I have no idea why the results are so different from my expectation. Therefore, would like to seek advice from the community on:
- What is the issue of the ATAC-seq library? Is it library preparation error, sequencing error, or wrong analysis pipeline used?
- Is it worth conducting downstream analysis on this library preparation? (I did a crude analysis on DiffBind using all default setting, and found no differences by DESeq2 while 8 significant results from EdgeR)
Here are some diagnostic plots you may found it useful:
I got around 200000 peaks for each sample. And here is the some of the typical TSS enrichment plot:
I found that there is an enrichment of fragment at around 150-200bp:
However, I found that this might be actually normal for frozen mouse liver tissue (the tissue I used) from a scientific data publication:
The same "contamination" can also be visualized in M-plot:
I checked the peaks around Gapdh locus and found that seems the data is contaminated with noise.
Thanks in advance!