ChIP-seq流程结果文件解读

接前面文章：ChIP-seq | ATAC-seq | RNA-seq | 数据分析流程

前面已经把pipeline跑完了，但是关于结果的解读还是不清楚，这里来深入探讨一下。

 

复习：

• pipeline：https://github.com/ENCODE-DCC/chip-seq-pipeline2
• 大致流程图：https://www.encodeproject.org/pipelines/ENCPL272XAE
• chip-seq教程：Introduction to ChIP-Seq using high-performance computing
• 教程课时清单
• 课程公众号中文翻译版

 

输入文件：~/project/epigenetic/analysis/ChIP-seq/encode-pipeline/encc/H3K27ac/encc.chip.full.json

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"chip.title" : "hENCC ChIP-seq (H3K27ac)", "chip.description" : "ENCC-K27-2_1,ENCC-I1_1 (1st); ENCC-K27-1_1,ENCC-I2_1 (2st) ",   "chip.pipeline_type" : "histone", "chip.aligner" : "bowtie2", "chip.align_only" : false, "chip.true_rep_only" : false,   "chip.genome_tsv" : "~/softwares/chip-seq-pipeline2/db/hg19.tsv",   "chip.paired_end" : true, "chip.ctl_paired_end" : true,   "chip.fastqs_rep1_R1" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-K27-2_1.fastq.gz" ], "chip.fastqs_rep1_R2" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-K27-2_2.fastq.gz" ], "chip.fastqs_rep2_R1" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-K27-1_1.fastq.gz" ], "chip.fastqs_rep2_R2" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-K27-1_2.fastq.gz" ],   "chip.ctl_fastqs_rep1_R1" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I1_1.fastq.gz" ], "chip.ctl_fastqs_rep1_R2" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I1_2.fastq.gz" ], "chip.ctl_fastqs_rep2_R1" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I2_1.fastq.gz" ], "chip.ctl_fastqs_rep2_R2" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I2_2.fastq.gz" ],

　　

输出文件：

Output specification for chip.wdl - 解释了每一个后缀的文件是什么

 

所有中间文件【目录里面记录了具体的脚本的输出文件，可以慢慢查看】：

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call-align               call-call_peak_pooled  call-filter_ctl          call-macs2_signal_track_pooled  call-pool_ta_pr2 call-align_ctl           call-call_peak_ppr1    call-filter_R1           call-overlap                    call-qc_report call-align_R1            call-call_peak_ppr2    call-fraglen_mean        call-overlap_ppr                call-read_genome_tsv call-bam2ta              call-call_peak_pr1     call-gc_bias             call-overlap_pr                 call-reproducibility_overlap call-bam2ta_ctl          call-call_peak_pr2     call-idr_ppr             call-pool_ta                    call-spr call-bam2ta_no_dedup_R1  call-choose_ctl        call-jsd                 call-pool_ta_ctl                call-xcor call-call_peak           call-filter            call-macs2_signal_track  call-pool_ta_pr1                metadata.json

　　

 

了解一下每一步干了什么

• chip.align：比对
• chip.filter：过滤
• chip.bam2ta：converts sequence alignments in BAM format into BED，参考
• chip.spr：
• chip.jsd：
• chip.xcor：cross-correlation，参考
• chip.call_peak：callpeak命令，peak calling
• chip.macs2_signal_track：bdgcmp命令，signal generation
• chip.filter_picard_java
• chip.gc_bias_picard_java

 

pipeline的流程图：github备份 HTML

 

tagAlign.gz是什么文件，干什么用的？sequencing tags

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chr13   99073542        99073643        N       1000    + chr13   99073563        99073664        N       1000    - chr11   122621369       122621470       N       1000    - chr11   122621361       122621462       N       1000    + chr8    49450819        49450920        N       1000    + chr8    49450886        49450987        N       1000    -