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- #######################
- # globe
- #######################
- PEAKSNAKE_HOME: /home/zhxd/workspace/20231225_ChIP_ATAC/PeakSnake
- genome: ref/hg38.fa
- gtf: ref/genes_longest.gtf
- tss_tes_bed: ref/genes_longest.bed6
- tss_tes_shuffle_bed: ref/genes_shuffle.bed6
- seq_type: PE # 或者 "PE"
- peak_type: broad # narrow | broad
- # 有效基因组大小, 参考 https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html#effective-genome-size
- gsize: 2913022398
- # idr: 只支持 2 重复,适合 narrowPeak) ; intersect (2 + 重复 ) ; norep: 没有重复
- peak_selection: norep
- #######################
- # samples
- #######################
- samples:
- Diabetic_hs_rep1:
- Healthy_hs_rep1:
- contrasts:
- - Diabetic_hs_vs_Healthy_hs
- #######################
- # fastp
- #######################
- fastp: "--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --qualified_quality_phred 20 --length_required 50"
- #######################
- # bowtie2
- # PE 建议设置 --no-mixed --no-discordant, 只保留成对比对
- # ATAC-seq 必须设置 --maxins 1000 ~ 2000
- #######################
- bowtie2_index: ref/genome # 不设置则从genome.fa 构建
- bowtie2: --no-mixed --no-discordant --maxins 1000
- #######################
- # alignmentSieve
- # blackregion: 黑名单区域 线粒体 叶绿体 大肠杆菌等
- #######################
- alignmentSieve:
- minMappingQuality: 25
- blacklist: ref/hg38.blacklist.bed
- extra:
- #######################
- # bam to bw
- #######################
- bamCoverage: "--binSize 10 --normalizeUsing RPKM"
- #######################
- # MACS3
- # fold: 用于过滤 peaks
- # qscore: 用于过滤 peaks
- # macs3 callpeak ChIP-seq 一般不需要设置特殊参数
- # ATAC-seq 推荐: --nomodel --shift -100 --extsize 200 或 --nomodel --shift -75 --extsize 150
- # --SPMR -B 用于生成单碱基的 bdg 文件, 可以转换为 bw 文件,有可视化的需求可以加
- #######################
- macs3:
- qscore: 3
- extra: --nomodel --shift -100 --extsize 200 --SPMR -B
- #######################
- # replicate intersect
- #######################
- intersect:
- min_overlap: 0.5
- #######################
- # IDR
- #######################
- idr:
- idr_threshold: 0.05
- #######################
- # 提取序列用于 motif 分析
- #######################
- motif:
- top_n: 1000
- summit_flank: 50
- databases: motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme
- #######################
- # Peank 注释
- # 只关注 TSS 附近 用 ChIPseeker
- # 否则UROPA
- #######################
- uropa:
- do: yes
- feature: ['gene']
- feature_anchor: ['start']
- relative_location: ['Upstream', 'Downstream', 'OverlapStart', 'OverlapEnd','PeakInsideFeature', 'FeatureInsidePeak']
- distance: [2000, 500]
- #######################
- # footprinting
- #######################
- footprint:
- do: yes
- motif: motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme
- #######################
- # diff analysis
- #######################
- diff_peaks:
- do: yes
- method: edgeR # edgeR | DESeq2
- padj: 0.05
- extra: --dispersion 0.1
- #######################
- # cross correlation
- # ChIP-seq 需要进行, ATAC-seq 不需要
- #######################
- cross_correlation:
- do: no
- spp: "-s=0:5:500"
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