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bioRxiv · 10.1101/2022.12.15.520671

DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms

Shrestha, A. M. S.·Santiago, K. C. L.
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Abstract

BackgroundConventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning RNA-seq reads to a protein database, and demonstrated drastic improvements in speed, memory usage, and accuracy in identifying differentially expressed genes. ResultHere we report a further speed-up by replacing DNA-protein alignment by quasi-mapping, making our pipeline > 1000 x faster than assembly-based approach, and still more accurate. We also compare quasi-mapping to other mapping techniques, and show that it is faster but at the cost of sensitivity. ConclusionWe provide a quick-and-dirty differential gene expression analysis pipeline for non-model organisms without a reference transcriptome, which directly quasi-maps RNA-seq reads to a reference protein database, avoiding computationally expensive transcriptome assembly.

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Shrestha, A. M. S., Santiago, K. C. L.. 2022-12-19. DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms. https://doi.org/10.1101/2022.12.15.520671

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