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bioRxiv · 10.1101/313999

SQuIRE: Software for Quantifying Interspersed Repeat Elements

Yang, W. R.·Ardeljan, D.·Pacyna, C. N.·Payer, L. M.·Burns, K. H.
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Abstract

Transposable elements are interspersed repeat sequences that make up much of the human genome. Conventional approaches to RNA-seq analysis often exclude these sequences, fail to optimally adjudicate read alignments, or align reads to interspersed repeat consensus sequences without considering these transcripts in their genomic contexts. As a result, repetitive sequence contributions to transcriptomes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), an RNA-seq analysis pipeline that integrates repeat and genome annotation (RepeatMasker), read alignment (STAR), gene expression (StringTie) and differential expression (DESeq2). SQuIRE uniquely provides a locus-specific picture of interspersed repeat-encoded RNA expression. SQuIRE can be downloaded at (github.com/wyang17/SQuIRE).

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Yang, W. R., Ardeljan, D., Pacyna, C. N., Payer, L. M., Burns, K. H.. 2018-05-04. SQuIRE: Software for Quantifying Interspersed Repeat Elements. https://doi.org/10.1101/313999

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