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\"condition\"\n lfc_null: 1.0\n alt_hypothesis: \"greaterAbs\"\n point_width: 20\n mincount: 10\n alpha: 0.05\n threshold_plot: 10\n colormap: \"Blues\"\n figtype: \"png\"\n batch_effect:\n - \"\"\n\nisoform_analysis:\n FLAIR: true\n qscore: 1\n exp_thresh: 10\n col_opts: \"--annotation_reliant generate --generate_map --stringent\"\n\nprotein_annotation:\n lambda: false\n uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"\n num_matches: 3" } ] }, { "@id": "https://w3id.org/np/RA5KG-dXAGOjbML0VetA_U28YGm82FIiDCK2AyJA-f-Ts/dataset", "@type": [ "https://schema.org/Dataset" ], "https://w3id.org/np/snakemake/describesWorkflow": [ { "@value": "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" } ], "https://w3id.org/np/snakemake/description": [ { "@value": "
\nThis workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.\nFirst a transcriptome FASTA is constructed using gffread. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2.\nNext quantification is performed using salmon before normalization and differential expression analysis are conducted by PyDESeq2.\nThe workflow can optionally analyze splice-isoforms through integrating the FLAIR workflow.\nAdditionaly, NanoPlot is employed to analyze initial sequencing data and QualiMap is used to evaluate mapping results.\n