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. Author manuscript; available in PMC: 2023 Aug 1.
Published in final edited form as: Curr Protoc. 2022 Aug;2(8):e498. doi: 10.1002/cpz1.498

Figure 6. Library quality control.

Figure 6.

Libraries should be screened using an electrophoresis instrument such as the Agilent Bioanalyzer prior to sequencing to verify that the DNA fragment size falls within the expected range of the protocol. (A) One common pitfall of scRNA-seq libraries is degraded cDNA from dead or lysed cells, visualized by a shift in the molecular weight towards 1,000 bp and below. (B) Abundant PCR adapter artifacts can also swamp out gene-body reads, resulting in poor quality libraries, as visualized by reduced estimated number of genes detected per cell. (C, right) Likewise, ATAC-seq libraries should be checked for the expected “nucleosome ladder” pattern. Under-tagmented libraries (C, left) can be size-selected to yield an acceptable profile for sequencing.