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• W2963235910 abstract "Abstract Motivation LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify RNA at specific LINE-1 loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA. Results We provide a tool, L1-EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1-EM on simulated data and against long read sequencing from HEK cells. Availability L1-EM is written in python. The source code along with the necessary annotations are available at https://github.com/FenyoLab/L1EM and distributed under GPLv3. Contact wilson.mckerrow@nyulangone.org , david@fenyolab.org" @default.
• W2963235910 created "2019-07-30" @default.
• W2963235910 creator A5054597616 @default.
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• W2963235910 date "2019-07-24" @default.
• W2963235910 modified "2023-09-23" @default.
• W2963235910 title "L1EM: A tool for accurate locus specific LINE-1 RNA quantification" @default.
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• W2963235910 doi "https://doi.org/10.1101/714014" @default.
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