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LasTEq: long-read assisted short-read TE quantification [long]

ABSTRACT: With an ability to compromise genome integrity, transposable elements (TEs) have significant associations with human diseases. Short-read sequencing has been used to study the expression of TEs; however, the highly repetitive nature of these elements makes multimapping a critical issue. Here we implement lasTEq, an improved quantification method by integrating long-read sequencing. Introducing computed transcript per million(TPM) counts from long-read sequencing as prior distribution during Expectation-Maximization(EM) model in short-read TE quantification, multi-mapped reads are re-assigned to correct expression values. Based on simulated short reads, lasTEq outperforms current quantitative approaches and is significantly favorable in capturing newly inserted TEs. We also verified that TEs quantified by lasTEq clearly related to euchromatins and heterochromatins in cell line samples. With lasTEq we anticipate that more accurate quantification can be performed, allowing novel functions of TEs to be uncovered.

ORGANISM(S): Homo sapiens

PROVIDER: GSE225377 | GEO | 2023/09/01

REPOSITORIES: GEO

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lasTEq: long-read assisted short-read TE quantification [short]

Project description:With an ability to compromise genome integrity, transposable elements (TEs) have significant associations with human diseases. Short-read sequencing has been used to study the expression of TEs; however, the highly repetitive nature of these elements makes multimapping a critical issue. Here we implement lasTEq, an improved quantification method by integrating long-read sequencing. Introducing computed transcript per million(TPM) counts from long-read sequencing as prior distribution during Expectation-Maximization(EM) model in short-read TE quantification, multi-mapped reads are re-assigned to correct expression values. Based on simulated short reads, lasTEq outperforms current quantitative approaches and is significantly favorable in capturing newly inserted TEs. We also verified that TEs quantified by lasTEq clearly related to euchromatins and heterochromatins in cell line samples. With lasTEq we anticipate that more accurate quantification can be performed, allowing novel functions of TEs to be uncovered.

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