TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments

Autor:	Federico Ansaloni, Nicolò Gualandi, Mauro Esposito, Stefano Gustincich, Remo Sanges
Rok vydání:	2022
Předmět:	Statistics and Probability Computational Mathematics Consensus Bias Computational Theory and Mathematics Settore BIO/13 - Biologia Applicata DNA Transposable Elements High-Throughput Nucleotide Sequencing RNA-Seq Molecular Biology Biochemistry Computer Science Applications
Zdroj:	Bioinformatics. 38:4430-4433
ISSN:	1367-4811 1367-4803
DOI:	10.1093/bioinformatics/btac526
Popis:	Summary Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. Availability and implementation The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). Supplementary information Supplementary data are available at Bioinformatics online.
Databáze:	OpenAIRE
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