https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/Head https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/assertion https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/provenance https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/pubinfo https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/assertion https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/config-1 http://purl.org/dc/terms/identifier config.yml https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/config-1 https://schema.org/text samples: samples.csv ref: species: "Drosophila melanogaster" genome: "" annotation: "" accession: "GCF_000001215.4" ensembl_species: "" # e.g., "homo_sapiens" build: "" # e.g., "GRCh38" release: "" # e.g., "105" read_filter: min_length: 200 minimap2: index_opts: "" opts: "" maximum_secondary: 100 secondary_score_ratio: 1.0 samtools: samtobam_opts: "-b" bamsort_opts: "" bamindex_opts: "" bamstats_opts: "" quant: salmon_libtype: "U" deseq2: fit_type: "" design_factors: - "condition" lfc_null: 1.0 alt_hypothesis: "greaterAbs" point_width: 20 mincount: 10 alpha: 0.05 threshold_plot: 10 colormap: "Blues" figtype: "png" batch_effect: - "" isoform_analysis: FLAIR: true qscore: 1 exp_thresh: 10 col_opts: "--annotation_reliant generate --generate_map --stringent" protein_annotation: lambda: false uniref: "https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz" num_matches: 3 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/dataset http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://schema.org/Dataset https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/dataset https://w3id.org/np/snakemake/describesWorkflow RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/dataset https://w3id.org/np/snakemake/description This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology. First a transcriptome FASTA is constructed using gffread [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2]. Next 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]. The workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow. Additionaly, 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/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/dataset https://w3id.org/np/snakemake/generatedAt 2026-04-17T13:29:12.172652+00:00 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/dataset https://w3id.org/np/snakemake/hasConfigurationSection https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/workflow-configuration https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/workflow-configuration http://www.w3.org/2000/01/rdf-schema#label from workflow configuration https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/workflow-configuration https://w3id.org/np/snakemake/hasConfigurationFile https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/config-1 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/provenance https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/assertion http://www.w3.org/ns/prov#generatedAtTime 2026-04-17T15:29:13.310830 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/assertion http://www.w3.org/ns/prov#wasAttributedTo https://orcid.org/0000-0003-2408-7588 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/pubinfo https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://purl.org/dc/terms/created 2026-04-17T13:29:12.172652+00:00 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://purl.org/dc/terms/creator https://orcid.org/0000-0003-2408-7588 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://purl.org/nanopub/x/hasNanopubType https://schema.org/Dataset https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://purl.org/nanopub/x/signedBy https://orcid.org/0000-0003-2408-7588 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.w3.org/2000/01/rdf-schema#label Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.w3.org/ns/prov#generatedAtTime 2026-04-17T15:29:13.310830 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU http://www.w3.org/ns/prov#wasAttributedTo https://orcid.org/0000-0003-2408-7588 https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/sig http://purl.org/nanopub/x/hasAlgorithm RSA https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/sig http://purl.org/nanopub/x/hasPublicKey MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/sig http://purl.org/nanopub/x/hasSignature YKX/2GkgL2KAQ1jHXfHDW511vSbWE34aFAaBQdpQeAZkdVvVnNYVDYiFCHjjb1KuRX2M6DWnOb4PAbZpb8fG8ET+ws6jO4YTKnyGFJZ13tbfB5stXwgfcz53mJ36XYeLvrUuSkmjIUFRkTxZDzKZNCPsloE0STs5tEg9lmqyG0rhEMQhFXONmyd5IOgFCa6r2MMG/NCqhXWxqRP4p5D7dB3RQTJrmwDazF2uZQbtSTPF0Hf0c8BhN8XPO4vABpFVf0R6La5HATARUSSCwIZQLdW6edt6M4Fa0hXGYWQJ9/uslSvDTtWkjJPdeF5OIMFCVEPxBNmJuJ3md23cad5E6g== https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/sig http://purl.org/nanopub/x/hasSignatureTarget https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU https://w3id.org/np/RA3zvGFqSf85lp0U4j3ytqZTxo8A07Vv8V5tqqpkGRvnU/sig http://purl.org/nanopub/x/signedBy https://orcid.org/0000-0003-2408-7588