http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#Head
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.nanopub.org/nschema#hasAssertion
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#assertion
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.nanopub.org/nschema#hasProvenance
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#provenance
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.nanopub.org/nschema#hasPublicationInfo
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#pubinfo
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
http://www.nanopub.org/nschema#Nanopublication
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#assertion
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#config-1
http://purl.org/dc/terms/identifier
config.yml
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#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
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#dataset
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
https://schema.org/Dataset
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#dataset
https://w3id.org/np/snakemake/describesWorkflow
RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#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. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2.
Next quantification is performed using salmon before normalization and differential expression analysis are conducted by PyDESeq2.
The workflow can optionally analyze splice-isoforms through integrating the FLAIR workflow.
Additionaly, NanoPlot is employed to analyze initial sequencing data and QualiMap is used to evaluate mapping results.
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#dataset
https://w3id.org/np/snakemake/generatedAt
2026-04-16T13:18:51.156570+00:00
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#dataset
https://w3id.org/np/snakemake/hasConfigurationSection
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#workflow-configuration
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#workflow-configuration
http://www.w3.org/2000/01/rdf-schema#label
from workflow configuration
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#workflow-configuration
https://w3id.org/np/snakemake/hasConfigurationFile
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#config-1
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#provenance
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#assertion
http://www.w3.org/ns/prov#generatedAtTime
2026-04-16T15:18:53.047964
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#assertion
http://www.w3.org/ns/prov#wasAttributedTo
https://orcid.org/0000-0003-2408-7588
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#pubinfo
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#sig
http://purl.org/nanopub/x/hasAlgorithm
RSA
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#sig
http://purl.org/nanopub/x/hasPublicKey
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#sig
http://purl.org/nanopub/x/hasSignature
NdCHOSpUEIl1KaT/altd2+bO+0Wy5JprB6HNMcj9XSpCoJiOPyrwWih69c2qU6/0ElbCDrS4JCsMq37F1y1ntTpM3m6vAd6B6Olv/7JBa1WDwqha8DW3o8qV7TBhBTeEfTSPAW88Ep1MzWun0Sv9+gvIDT+RnYfJKvpieGiKqeXskeqR8KCt2UYHjWKuv/2yHmstycnw2Q+2Q44ogs8f1EFL2lT1zT7WJHFopMtXcgxt9+IDLWceQnKzm6348nKOb0scBahnscbzCWkmrQNz9HsuxzTD3QPAh7CQq2vUufm2dweY3rJOLlZ20Vv4Y1ZfGPFpe1/Ba5xuKupBre09eA==
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY#sig
http://purl.org/nanopub/x/hasSignatureTarget
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://purl.org/dc/terms/created
2026-04-16T13:18:51.156570+00:00
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://purl.org/dc/terms/creator
https://orcid.org/0000-0003-2408-7588
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://purl.org/nanopub/x/hasNanopubType
https://schema.org/Dataset
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.w3.org/2000/01/rdf-schema#label
Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.w3.org/ns/prov#generatedAtTime
2026-04-16T15:18:53.047964
http://purl.org/np/RA7OmRK6Pu0TsndGzT0nRar_9YOy-dkFmDYOU3J1ZuuWY
http://www.w3.org/ns/prov#wasAttributedTo
https://orcid.org/0000-0003-2408-7588