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
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.
Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE