I am recently applying some customized anlysis. Brefly, this protocol remove linear chromosome for human genomic unless some genmic intervals been protection from DNase digestion because of special structure, ( a bit like DNase-seq?, only this genmic intervals not protect by histone but other factor). So, I expect I wiil get a list of peaks from NGS results.
Tricky thing is that the number of peaks I get greatly surpassed the amount we estimated from the existing biological knowledge. So is noise introduced due to wet experiments or improper sequencing procedures?
I applied estimateLibComplexity (a library complexity evaluation in ATACseqQC) to evaluate wheather the sequence depth is saturation? and I got following resuslts.
I have read the article published on bmcgenomics (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4559-3) , I noticed the fig. 4 shows diiferent library complexity analysis results, but I still cant confirm whether my results are saturated？
If its saturated, please allow me ask more question.
Q: If we assume that there are still remain undigestion a little amount of linear genomic DNA in the sample, will a saturated sequencing could introduce more noise from the linear genome?
Thanks for your attention and kindly help. If I make any mistakes, please feel free to quote it directly.