接前面文章：ChIP-seq | ATAC-seq | RNA-seq | 數據分析流程
前面已經把pipeline跑完了，但是關於結果的解讀還是不清楚，這里來深入探討一下。
復習：
- pipeline：https://github.com/ENCODE-DCC/chip-seq-pipeline2
- 大致流程圖：https://www.encodeproject.org/pipelines/ENCPL272XAE
- chip-seq教程：Introduction to ChIP-Seq using high-performance computing
- 教程課時清單
- 課程公眾號中文翻譯版
輸入文件：~/project/epigenetic/analysis/ChIP-seq/encode-pipeline/encc/H3K27ac/encc.chip.full.json
"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" ],
輸出文件：
Output specification for chip.wdl - 解釋了每一個后綴的文件是什么
所有中間文件【目錄里面記錄了具體的腳本的輸出文件，可以慢慢查看】：
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：比對
- chip.filter：過濾
- chip.bam2ta：converts sequence alignments in BAM format into BED，參考
- chip.spr：
- chip.jsd：
- chip.xcor：cross-correlation，參考
- 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的流程圖：github備份 HTML
tagAlign.gz是什么文件，干什么用的？sequencing tags
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 -