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Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2].\nNext quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2].\nThe workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow.\nAdditionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results." } ], "https://w3id.org/np/snakemake/generatedAt": [ { "@value": "2026-05-05T18:00:57.134252+00:00", "@type": "http://www.w3.org/2001/XMLSchema#dateTime" } ], "https://w3id.org/np/snakemake/hasConfigurationSection": [ { "@id": 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