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Runs project-specific BLAZE demultiplexing for ONT long-read single-cell RNA-seq, including barcode and UMI detection, whitelist generation, chemistry confirmation, and demultiplexed FASTQ production.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Runs project-specific ONT-only FLAIR transcriptome generation, optional multi-sample combine, quantification, and post-quantification single-cell matrix recovery with recover_sc_matrix.py.
Summarizes completed long-read single-cell RNA-seq runs using deep results-style integrative writing, with emphasis on post-annotation isoform analysis, sequence-model outputs, transcript-level events, gene-function interpretation, and literature-grounded condition-specific consequences.
Uses Orthrus transcript-sequence embeddings plus pretrained regression and classification heads to predict isoform-level functional properties for one gene at a time in a persistent tmux shell session.
Draws gene-level sashimi plots from per-sample BAM files after downstream annotation by extracting group-specific cell barcodes from a Seurat object, subsetting BAMs by barcode tag, building ggsashimi input tables, and iteratively plotting one gene at a time in tmux.
Adds the merged isoform count assay and isoform UMAP from a merged isoform Seurat object into a merged gene Seurat object, then saves a new combined Seurat RDS for joint downstream gene-plus-isoform analysis.
Performs downstream cell type annotation for the project in one persistent tmux R session, including cluster UMAP review, cluster-level marker discovery for gene and isoform assays, optional automatic annotation with ScType, optional manual cluster renaming, celltype-level differential analysis, heatmaps, enrichment, and cell composition summaries.
| name | blaze-demultiplex |
| description | Runs project-specific BLAZE demultiplexing for ONT long-read single-cell RNA-seq, including barcode and UMI detection, whitelist generation, chemistry confirmation, and demultiplexed FASTQ production. |
Use this skill for the ONT barcode and UMI preprocessing step.
Primary skill file:
./SKILL.mdONTblaze conda environment for this skill's commands.--kit-version--full-bc-whitelist and --umi-lentmux session.conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then conda activate blaze.tmux session name, and wait for confirmation.tmux session until the BLAZE command has finished.tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.01_blaze as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.Do not surface low-level tuning unless the user asks or troubleshooting requires it.