ATAC seq no 150bp fragment
Hello eveyone, i have a very strange problem. I have some atac seq data, but when i try to plot the fragment distribution, i found thereis a gap near 150bp, which means there is no 150bp-length fragment. I cant understand why that is.
The workflow of experiment and bioinformatics is the same with what we did before. Maybe the tissue sample led to its creation? Besides, the fqs of the all samples showed a high duplicated sequence level. Is this the reason?
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Does this plot include reads mapping to chrM, and if so exclude chrM reads and repeat it. High duplication can either be due to lots of chrM reads since that genome is so small, or because the library is poor.
Sorry for late reply and tanks for youre advice! I have removed ChrM reads before plotting, and I think high duplication may be due to overmuch PCR cycle. But why high duplication could influence the gap? The gap length is constant among these 9 samples. This picture is plotted before sequencing and it looks good.