rows { options { physical_type: PHYSICAL_STREAM_TYPE_QUADS max_name_table_size: 128 max_prefix_table_size: 16 max_datatype_table_size: 16 logical_type: LOGICAL_STREAM_TYPE_DATASETS version: 2 } } rows { prefix { value: "http://purl.org/dc/terms/" } } rows { name { } } rows { namespace { name: "dcterms" value { prefix_id: 1 } } } rows { prefix { value: "http://www.nanopub.org/nschema#" } } rows { namespace { name: "np" value { prefix_id: 2 name_id: 1 } } } rows { prefix { value: "http://purl.org/nanopub/x/" } } rows { namespace { name: "npx" value { prefix_id: 3 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/snakemake/" } } rows { namespace { name: "ns1" value { prefix_id: 4 name_id: 1 } } } rows { prefix { value: "https://orcid.org/" } } rows { namespace { name: "orcid" value { prefix_id: 5 name_id: 1 } } } rows { prefix { value: "http://www.w3.org/ns/prov#" } } rows { namespace { name: "prov" value { prefix_id: 6 name_id: 1 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { namespace { name: "rdfs" value { prefix_id: 7 name_id: 1 } } } rows { prefix { value: "https://schema.org/" } } rows { namespace { name: "schema" value { prefix_id: 8 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/RA5KG-dXAGOjbML0VetA_U28YGm82FIiDCK2AyJA-f-Ts/" } } rows { namespace { name: "sub" value { prefix_id: 9 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/" } } rows { name { value: "RA5KG-dXAGOjbML0VetA_U28YGm82FIiDCK2AyJA-f-Ts" } } rows { namespace { name: "this" value { prefix_id: 10 } } } rows { prefix { value: "http://www.w3.org/2001/XMLSchema#" } } rows { namespace { name: "xsd" value { prefix_id: 11 name_id: 1 } } } rows { name { value: "hasAssertion" } } rows { name { value: "assertion" } } rows { name { value: "Head" } } rows { quad { s_iri { prefix_id: 10 } p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } g_iri { } } } rows { name { value: "hasProvenance" } } rows { name { value: "provenance" } } rows { quad { p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } } } rows { name { value: "hasPublicationInfo" } } rows { name { value: "pubinfo" } } rows { quad { p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } } } rows { prefix { value: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" } } rows { name { value: "type" } } rows { name { value: "Nanopublication" } } rows { quad { p_iri { prefix_id: 12 } o_iri { prefix_id: 2 } } } rows { name { value: "config-1" } } rows { name { value: "identifier" } } rows { quad { s_iri { prefix_id: 9 } p_iri { prefix_id: 1 } o_literal { lex: "config.yml" } g_iri { prefix_id: 9 name_id: 4 } } } rows { name { value: "text" } } rows { quad { p_iri { prefix_id: 8 name_id: 14 } o_literal { lex: "samples: samples.csv\n\nref:\n species: \"Drosophila melanogaster\"\n genome: \"\"\n annotation: \"\"\n accession: \"GCF_000001215.4\"\n ensembl_species: \"\" # e.g., \"homo_sapiens\"\n build: \"\" # e.g., \"GRCh38\"\n release: \"\" # e.g., \"105\"\n\nread_filter:\n min_length: 200\n\nminimap2:\n index_opts: \"\"\n opts: \"\"\n maximum_secondary: 100\n secondary_score_ratio: 1.0\n\nsamtools:\n samtobam_opts: \"-b\"\n bamsort_opts: \"\"\n bamindex_opts: \"\"\n bamstats_opts: \"\"\n\nquant:\n salmon_libtype: \"U\"\n\ndeseq2:\n fit_type: \"\"\n design_factors:\n - \"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" } } } rows { name { value: "dataset" } } rows { name { value: "Dataset" } } rows { quad { s_iri { prefix_id: 9 } p_iri { prefix_id: 12 name_id: 10 } o_iri { prefix_id: 8 name_id: 16 } } } rows { name { value: "describesWorkflow" } } rows { quad { p_iri { prefix_id: 4 } o_literal { lex: "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" } } } rows { name { value: "description" } } rows { quad { p_iri { } o_literal { lex: "
\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