ArticleBMC bioinformatics2024
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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× 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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