Basics of ChIP-seq data analysis

https://www.bioconductor.org/help/course-materials/2016/CSAMA/lab-5-chipseq/Epigenetics.html
Basics of ChIP-seq data analysis

夏目沉吟:
https://rpkgs.datanovia.com/ggpubr/reference/ggpie.html

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https://stackoverflow.com/questions/3397885/how-do-you-read-in-multiple-txt-files-into-r

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https://www.genome.ucsc.edu/FAQ/FAQformat.html

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Basics of ChIP-seq data analysis (bioconductor.org)

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https://www.bioconductor.org/help/course-materials/2016/CSAMA/lab-5-chipseq/Epigenetics.html
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https://gatk.broadinstitute.org/hc/en-us

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https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows

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https://cloud.tencent.com/developer/article/1442293

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https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

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https://rdrr.io/bioc/DiffBind/man/dba.count.html

https://www.jianshu.com/p/6932c72aba63

高通量测序数据处理学习记录（二）：Read Counts的提取
https://www.jianshu.com/p/7cc5df9f7900

https://www.jianshu.com/p/1c66cfb423af高通量测序数据处理学习记录（七）：使用ChIPQC包检查ChIP-seq的质量

ChIP-Seq分析之ChIPQC结果含义https://mp.weixin.qq.com/s?src=11&timestamp=1607082672&ver=2746&signature=5ImXBAlK9kcTKUY7huOQXQ8G5N8Ksdf3sEku4pnfsM5yWAXGmjJLhmr17ZwdevKzvfbmy0tw0tG*iimlMkA0AXS33iDiNIZhXGtZA5qI2s1uuvUB4iXPXpukAxuWHV1O&new=1

https://hbctraining.github.io/Intro-to-ChIPseq/lessons/06_combine_chipQC_and_metrics.html

测序深度的计算公式为LN/G，L就是读段长度，N是读段数目，G是基因组大小。
举例来说，人类基因组3.1G，一个RNA-seq的reads数据为20M，数据为paired-end，读长150bp，那么测序深度就是20M2150/3.1G= 2 X

那我们再来讨论一下sequencing depth 和 sequencing coverage的区别：
事实上没有区别，若是真要讲个说法，那就是coverage可以理解为检测到全基因组的多少区域（百分比，最大值为100%），但是sequencing covergae指的就是depth of sequencing coverage也就是sequencing depth，反映了一个区域被平均多少个reads检测到。
另外breadth of coverage需要区别一下，就是将全基因组大小换成target region作为分母计算上面那个公司，

https://mp.weixin.qq.com/s?src=11&timestamp=1607082672&ver=2746&signature=5ImXBAlK9kcTKUY7huOQXQ8G5N8Ksdf3sEku4pnfsM75IEeVr5rfDQAKLFlymvLs3glGw2Hlj272vbqcKu38y3ojgCVdcj82LdS6hFkZptOjYZC4wAudS49qLcFo4qwt&new=1ChIP-Seq数据质控之ChIPQC使用

https://www.plob.org/article/16026.html

https://www.jianshu.com/p/7027251a98fc GeneOverlap: 用于基因Overlap的检验及可视化R包

https://blog.csdn.net/u012110870/article/details/107907582

https://blog.csdn.net/weixin_43569478/article/details/108079450?ops_request_misc=%257B%2522request%255Fid%2522%253A%2522160709138519724838592357%2522%252C%2522scm%2522%253A%252220140713.130102334.pc%255Fall.%2522%257D&request_id=160709138519724838592357&biz_id=0&utm_medium=distribute.pc_search_result.none-task-blog-2_allfirst_rank_v2~rank_v29-1-108079450.nonecase&utm_term=chipseq%20overlap&spm=1018.2118.3001.4449

1. peak 在染色体上的分布
2. peak间的overlap分析

http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#overlap-of-peaks-and-annotated-genes
Overlap of peaks and annotated genes
Statistical testing of ChIP seq overlap
enrichPeakOverlap(queryPeak = files[[5]],
targetPeak = unlist(files[1:4]),
TxDb = txdb,
pAdjustMethod = “BH”,
nShuffle = 50,
chainFile = NULL,
verbose = FALSE)

第6篇：重复样本的处理——IDR
https://www.jianshu.com/p/d8a7056b4294

如何得到两个重复样本间一致性的peaks? 一种简单粗暴的方法就是用bedtools计算peaks的overlaps。

bedtools intersect
-a macs2/Nanog-rep1_peaks.narrowPeak
-b macs2/Nanog-rep2_peaks.narrowPeak
-wo > bedtools/Nanog-overlaps.bed