Transposable elements (TE) are mobile genetic elements that can readily change their genomic position. When not properly silenced, TEs can contribute a substantial portion to the cell’s transcriptome, but are typically ignored in most RNA-seq data analyses. One reason for leaving TE-derived reads out of RNA-seq analyses is the complexities involved in properly aligning short sequencing reads to these highly repetitive regions. Here we describe a method for including TE-derived reads in RNA-seq differential expression analysis using an open source software package called TEtranscripts. TEtranscripts is designed to assign both uniquely and ambiguously mapped reads to all possible gene and TE-derived transcripts in order to statistically infer the correct gene/TE abundances. Here, we provide a detailed tutorial of TEtranscripts using a published qPCR validated dataset.
CITATION STYLE
Jin, Y., & Hammell, M. (2018). Analysis of RNA-seq data using tetranscripts. In Methods in Molecular Biology (Vol. 1751, pp. 153–167). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7710-9_11
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