数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-workflows-atacseq-pipeline

维护者 FreedomIntelligence · 最近更新 2026年4月1日

ATAC-seq: trimming → alignment → peak calling → differential.

OpenClawNanoClaw分析处理复现实验bio-workflows-atacseq-pipeline🧠 bioos extended suitebioos extended bioinformatics suiteatac

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-atacseq-pipeline

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

Complete workflow ，面向 raw ATAC-seq FASTQ files to accessibility peaks，differential analysis，、 TF footprinting。
NEXTERA_R1="CTGTCTCTTATACACATCT" NEXTERA_R2="CTGTCTCTTATACACATCT。
用于 sample in sample1 sample2 sample3；do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \ -o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz \ --adapter_sequence ${NEXTERA_R1} \ --adapter_sequence_r2 ${NEXTERA_R2} \ --qualified_quality_phred 20 \ --length_required 25 \ --html qc/${sample}_fastp.html done。

原始文档

SKILL.md 摘录

Build index (once)

bowtie2-build genome.fa bt2_index/genome

Align with ATAC-seq specific settings

for sample in sample1 sample2 sample3; do bowtie2 -p 8 -x bt2_index/genome
-1 trimmed/${sample}_R1.fq.gz
-2 trimmed/${sample}_R2.fq.gz
--very-sensitive
--no-mixed --no-discordant
-X 2000
2> aligned/${sample}.log |
samtools view -@ 4 -bS -q 30 -f 2 - |
samtools sort -@ 4 -o aligned/${sample}.bam done


## Step 3: BAM Processing

ATAC-seq requires special processing: removing mitochondrial reads, shifting reads for Tn5 insertion, and removing duplicates.

Alternative manual Tn5 shift with bedtools:
```bash

适用场景

Use bio-workflows-atacseq-pipeline ，用于 genomics 、 bioinformatics workflows。
Apply bio-workflows-atacseq-pipeline to sequencing，variant，或 omics analysis tasks。