Abstract
Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.
Original language | English |
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Title of host publication | Proceedings Annual Meeting of the Austrian Society for Biomedical Engineering 2021 |
Subtitle of host publication | ÖGBMT 2021 |
Publisher | Verlag der Technischen Universität Graz |
Pages | 95-98 |
Number of pages | 4 |
DOIs | |
Publication status | Published - 2021 |
Event | Annual Meeting of the Austrian Society of the Biomedical Engineering 2021: ÖGBMT 2021 - Graz University of Technology, Graz, Austria Duration: 30 Sept 2021 → 1 Oct 2021 https://oegbmt2021.tugraz.at/ |
Conference
Conference | Annual Meeting of the Austrian Society of the Biomedical Engineering 2021 |
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Abbreviated title | ÖGBMT 2021 |
Country/Territory | Austria |
City | Graz |
Period | 30/09/21 → 1/10/21 |
Internet address |
Keywords
- Transposable element
- enrichment
- ChIP-seq
- histone modifications