菜单
Runs project-specific minimap2 splice-aware alignment for long-read RNA-seq, primarily for ONT single-cell reads after BLAZE, with explicit preset selection, tag-preservation handling, and command confirmation.
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基于 SOC 职业分类
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 | minimap2-align |
| description | Runs project-specific minimap2 splice-aware alignment for long-read RNA-seq, primarily for ONT single-cell reads after BLAZE, with explicit preset selection, tag-preservation handling, and command confirmation. |
Use this skill for the genome-alignment step in the project workflow.
Primary skill file:
./SKILL.mdminimap2 conda environment for this skill's commands.-x splice for ONT-x splice:hq for PacBio CCS if alignment is explicitly requestedCB:Z and UB:Z tags into FASTQ comments, preserve them with -y.tmux session.conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then conda activate minimap2.tmux session name, and wait for confirmation.tmux session until the minimap2 command has finished.tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.02_minimap2 as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.minimap2 -ax splice -y -t <threads> ref.fa reads.fastq.gz > aln.sam