What is it about?
DEGoldS is a workflow consisting on sequential Bash and R scripts that allow the evaluation in terms of True positives and False Positives of bioinformatic Differential Expression analysis pipelines. This method uses RNA-seq realistic simulations to construct a Gold-Standard necessary for pipelines benchmarking.
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Why is it important?
When working when non-model species in bioinformatic analyses, specially in those species with complex genomes and with no publicly available reference, it is a common scenario to make modifications to standard pipelines. However, is difficult to assess how modifications affect the final result. In this context, several studies have been carried out to evaluate specific pipelines but there is not a general workflow for this purpose. DEGoldS can accommodate with a wide range of Differential Expression analysis bioinformatic pipelines and allows to assess their and their modifications’ effectiveness making an appropriate tool in pipeline optimization.
Perspectives
This research allowed us to decide our strategy to follow in Pinus radiata RNA-seq experiments. Results showed us that in our dataset small parameter tunings had big relevance in the final results.
Mikel Hurtado
Read the Original
This page is a summary of: DEGoldS: A Workflow to Assess the Accuracy of Differential Expression
Analysis Pipelines through Gold-standard Construction, Current Bioinformatics, May 2023, Bentham Science Publishers,
DOI: 10.2174/1574893618666230222122054.
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