Question: Enough cell number or not based on library complexity evaluation by ATACseqQC?
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9 weeks ago by
Gary10
Gary10 wrote:

Hi,

I use ATACseqQC to estimate the library complexity of one ATAC-Seq data. When I don't trim any reads, it seems that our library complexity (cell number) is not enough because of a saturation plateau (fig. 1). However, it appears that the library complexity (cell number) is enough because of an unsaturation curve, if I trim chrM, duplicate, low mapping quality, and improper reads (fig. 2). I don't know which one is correct. Could you help me? May I know how ATACseqQC estimates the number of putative sequenced fragments and distinct fragments beyond the number of reads we sequenced (i.e., about 27 million reads)? Many thanks.

Best,

Gary

Fig. 1. The library complexity based on untrimmed reads enter image description here

Fig. 2. The library complexity based on trimmed reads enter image description here

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