القائمة
Runs project-specific samtools sorting, indexing, quick structural validation, and optional flagstat summary to prepare long-read RNA alignments for downstream quantification.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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 | samtools-bam-processing |
| description | Runs project-specific samtools sorting, indexing, quick structural validation, and optional flagstat summary to prepare long-read RNA alignments for downstream quantification. |
Use this skill after alignment output exists and downstream tools require a sorted and indexed BAM.
Primary skill file:
./SKILL.mdsamtools conda environment for this skill's commands.samtools sort directly on aligner output unless the user explicitly wants intermediate BAMs.tmux session.conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then conda activate samtools.sort plus index, show the full command block and the planned tmux session name before execution.tmux session until the samtools command block has finished.tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.03_samtools as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.samtools sort -@ <threads> -o sample.sorted.bam sample.sam
samtools index sample.sorted.bam