. . . . "config.yml" . "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" . . "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "This 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 [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].\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." . "2026-04-17T15:19:46.851430+00:00"^^ . . . "QC/qualimap/barcode10" . "alignment_qa" . . "qualimap/barcode13/qualimapReport.html" . "alignment_qa_report" . . "qualimap/barcode15/qualimapReport.html" . "alignment_qa_report" . . "qualimap/barcode16/qualimapReport.html" . "alignment_qa_report" . . "sorted_alignments/barcode10_sorted.bam" . "bam_sort" . . "sorted_alignments/barcode11_sorted.bam" . "bam_sort" . . "sorted_alignments/barcode12_sorted.bam" . "bam_sort" . . "sorted_alignments/barcode13_sorted.bam" . "bam_sort" . . "sorted_alignments/barcode15_sorted.bam" . "bam_sort" . . "sorted_alignments/barcode16_sorted.bam" . "bam_sort" . . "QC/bamstats/barcode10.txt" . "bam_stats" . . "QC/qualimap/barcode11" . "alignment_qa" . . "QC/bamstats/barcode11.txt" . "bam_stats" . . "QC/bamstats/barcode12.txt" . "bam_stats" . . "QC/bamstats/barcode13.txt" . "bam_stats" . . "QC/bamstats/barcode15.txt" . "bam_stats" . . "QC/bamstats/barcode16.txt" . "bam_stats" . . "index/flair_genome_index.mmi" . "build_flair_genome_index" . . "index/transcriptome_index.mmi" . "build_minimap_index" . . "transcriptome/corrected_transcriptome.fa" . "correct_transcriptome" . . "counts/barcode10_salmon/quant.sf" . "count_reads" . . "counts/barcode11_salmon/quant.sf" . "count_reads" . . "QC/qualimap/barcode12" . "alignment_qa" . . "counts/barcode12_salmon/quant.sf" . "count_reads" . . "counts/barcode13_salmon/quant.sf" . "count_reads" . . "counts/barcode15_salmon/quant.sf" . "count_reads" . . "counts/barcode16_salmon/quant.sf" . "count_reads" . . "de_analysis/condition_wt_vs_mt_MA_plot.svg" . "de_analysis/condition_wt_vs_mt_count_heatmap.svg" . "de_analysis/condition_wt_vs_mt_dispersion_plot.svg" . "de_analysis/condition_wt_vs_mt_l2fc.tsv" . "de_analysis/condition_wt_vs_mt_sample_heatmap.svg" . "de_analysis/condition_wt_vs_mt_top_count_heatmap.svg" . "deseq2" . . "de_analysis/all.rds" . "de_analysis/normcounts.tsv" . "deseq2_init" . . "references/ncbi_dataset_annotation.zip" . "download_ncbi_annotation" . . "references/ncbi_dataset_genome.zip" . "download_ncbi_genome" . . "filter/barcode10_filtered.fq" . "filter_reads" . . "filter/barcode11_filtered.fq" . "filter_reads" . . "QC/qualimap/barcode13" . "alignment_qa" . . "filter/barcode12_filtered.fq" . "filter_reads" . . "filter/barcode13_filtered.fq" . "filter_reads" . . "filter/barcode15_filtered.fq" . "filter_reads" . . "filter/barcode16_filtered.fq" . "filter_reads" . . "iso_analysis/align/flair.bam" . "iso_analysis/align/flair.bam.bai" . "iso_analysis/align/flair.bed" . "flair_align" . . "iso_analysis/collapse/flair.isoforms.bed" . "iso_analysis/collapse/flair.isoforms.fa" . "flair_collapse" . . "iso_analysis/align/flair_all_corrected.bed" . "flair_correct" . . "iso_analysis/diffexp/genes_deseq2_QCplots_wt_v_mt.pdf" . "iso_analysis/diffexp/genes_deseq2_wt_v_mt.tsv" . "iso_analysis/diffexp/isoforms_deseq2_QCplots_wt_v_mt.pdf" . "iso_analysis/diffexp/isoforms_deseq2_wt_v_mt.tsv" . "iso_analysis/diffexp/isoforms_drimseq_wt_v_mt.tsv" . "flair_diffexp" . . "iso_analysis/plots" . "flair_plot_isoforms" . . "iso_analysis/quantify/flair.counts.tsv" . "flair_quantify" . . "QC/qualimap/barcode15" . "alignment_qa" . . "references/genomic.fa.fai" . "transcriptome/transcriptome.fa" . "genome_to_transcriptome" . . "references/genomic.gff" . "get_annotation" . . "references/genomic.fa" . "get_genome" . . "references/standardized_genomic.gtf" . "gff_to_gtf" . . "iso_analysis/report/isoforms" . "iso_analysis/report/usage" . "iso_analysis_report" . . "alignments/barcode10.sam" . "map_reads" . . "alignments/barcode11.sam" . "map_reads" . . "alignments/barcode12.sam" . "map_reads" . . "alignments/barcode13.sam" . "map_reads" . . "alignments/barcode15.sam" . "map_reads" . . "QC/qualimap/barcode16" . "alignment_qa" . . "alignments/barcode16.sam" . "map_reads" . . "merged/all_counts.tsv" . "merge_read_counts" . . "iso_analysis/reads_manifest.tsv" . "reads_manifest" . . "alignments/barcode10.bam" . "sam_to_bam" . . "alignments/barcode11.bam" . "sam_to_bam" . . "alignments/barcode12.bam" . "sam_to_bam" . . "alignments/barcode13.bam" . "sam_to_bam" . . "alignments/barcode15.bam" . "sam_to_bam" . . "alignments/barcode16.bam" . "sam_to_bam" . . "NanoPlot/barcode10/NanoPlot-report.html" . "sample_qa_plot" . . "qualimap/barcode10/qualimapReport.html" . "alignment_qa_report" . . "NanoPlot/barcode11/NanoPlot-report.html" . "sample_qa_plot" . . "NanoPlot/barcode12/NanoPlot-report.html" . "sample_qa_plot" . . "NanoPlot/barcode13/NanoPlot-report.html" . "sample_qa_plot" . . "NanoPlot/barcode15/NanoPlot-report.html" . "sample_qa_plot" . . "NanoPlot/barcode16/NanoPlot-report.html" . "sample_qa_plot" . . "references/standardized_genomic.gff" . "standardize_gff" . . "NanoPlot/NanoPlot-report.html" . "total_sample_qa_plot" . . "merged/all_counts_gene.tsv" . "merged/transcriptid_to_gene_plot.svg" . "transcriptid_to_gene" . . "qualimap/barcode11/qualimapReport.html" . "alignment_qa_report" . . "qualimap/barcode12/qualimapReport.html" . "alignment_qa_report" . "from workflow configuration" . . "2026-04-17T17:19:48.418353"^^ . . "2026-04-17T15:19:46.851430+00:00"^^ . . . . "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" . "2026-04-17T17:19:48.418353"^^ . . "RSA" . "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB" . "EY7zqSpVioJESS2rVe69TiAJj50TpZXJWXG5lTJvxYfi2zJb7c7N9rwA52maMFZsqvY2/AfqBO6fRcjQ5hDCiFisBtqcXw9rCU/8Oia9HQo/+wWLYKP4IbYX144l+IRLIhiNAOsYa/S+aG+gbCRaSwW0Yeem99qx2L80lDsKvcEs/Vb7LxgBNj08lYGYzZ4PucmUGY6l9/LX3bBPGH8MCaPxCjO2s+QS3G4PLVo+2KUR+zrV+BDlKPc+tnaB44fPwCIQO9L9QXJiAFCyCS9lhXCocCXW2g/2LIlut8QSR4RyVZSJKcRPEv/hGFf9SkQ+ca9v6cK2NUw4TAI1jHTBeQ==" . . .