Seminars, events & talks

Thursday, 17th February, 2022, 12:00

Analysis of transposable elements in R and Bioconductor with atena

PRBB Computational Genomics Seminar. Chair: Robert Castelo (Head of Functional Genomics Group).

Transposable elements (TEs) are DNA sequences that can mobilize within the genome either through a DNA intermediate, known as class II TEs or DNA transposons, or through an RNA intermediate, known as class I TEs or retrotransposons, as in the case of endogenous retroviruses (ERVs). Their insertions have resulted in a complex distribution of repeated elements occupying approximately half of the human genome and even higher proportions in other organisms such as plants. These elements have been described to be involved in physiological processes and human disease. TEs may exert their function through transcription, hence RNA sequencing can be used to detect their expression. However, due to their repetitive nature, reads sequenced from TE RNA transcripts usually map to multiple genomic loci and are consequently discarded in standard RNA sequencing data processing pipelines. For this reason we have developed atena, an open source software package for the analysis of TE expression in R, available at Bioconductor. The atena package re-implements in R three existing methods for TE expression quantification (TEtranscripts, ERVmap and Telescope), enabling the integration of TE expression analysis with a wide range of differential expression and functional analyses pipelines available in Bioconductor.

Zoom webinar: / Password: 788137

Speaker: Beatriz Calvo, Functional Genomics Group - Research Programme on Biomedical Informatics (GRIB, IMIM/UPF).

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