菜单
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Align bisulfite sequencing DNA methylation reads using Bismark only, with explicit validation of reference preparation, library layout detection, output organization, logging, and alignment QC. Use it for WGBS, RRBS, or other bisulfite-converted DNA methylation sequencing data when raw FASTQ files must be aligned before methylation extraction and downstream analysis.
Align ChIP-seq or ATAC-seq FASTQ files to a reference genome using Bowtie2, with strict input validation, library layout detection, output organization and logging. Use it when raw sequencing reads must be converted into sorted/indexed BAM files before downstream QC, peak calling, or footprinting.
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions such as promoters, exons, introns, intergenic regions, and TSS proximity, and generates visual summaries of feature distributions. ChIPseeker mode is also supported according to requirements.
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.
This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifies enrichment of known transcription factor binding motifs from established databases in genomic regions.
This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It provides workflows for chromatin state segmentation, model training, state annotation.
| name | ChIPseq-QC |
| description | Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics. |
This skill performs a full ChIP-seq quality control analysis from aligned BAM files and peak files.
Main steps include:
${proj_dir} in Step 0.${sample}.bam # filtered bam files
${sample}.narrowPeak # or broadPeak
all_chip_qc/
${sample}_spp.txt
${sample}_crosscorr.pdf
${sample}_frip.txt
Call:
mcp__project-init-tools__project_initwith:
sample: alltask: atac_qcThe tool will:
all_chip_qc directory.all_chip_qc directory, which will be used as ${proj_dir}.Call:
bam_file: Path to BAM fileoutput_dir: ${proj_dir}/Output: ${sample}_spp.txt, ${sample}_crosscorr.pdf
Call:
Output: ${sample}_frip.txt