教你学会ChIP-seq分析 | 第二讲

ChIP-seq的确是非常完善的NGS流程，各种资料层出不穷。

大家首先可以看下面几个完整流程的PPT来对ChIP-seq流程有个大致的印象，我对前面提到的文献数据处理的几个要点，就跟下面这个图片类似。

• QuEST is a statistical software for analysis of ChIP-Seq data with data and analysis results visualization through UCSC Genome Browser. http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html

• peak calling 阈值的选择： http://www.nature.com/nprot/journal/v7/n1/figtab/nprot.2011.420F2.html

• MeDIP-seq and histone modification ChIP-seq analysis http://crazyhottommy.blogspot.com/2014/01/medip-seq-and-histone-modification-chip.html

• 2011-review-ChIP-seq-high-quaility-data: http://www.nature.com/ni/journal/v12/n10/full/ni.2117.html?message-global=remove

• 不同处理条件的CHIP-seq的差异peaks分析： http://www.slideshare.net/thefacultyl/diffreps-automated-chipseq-differential-analysis-package

• 一个实际的CHIP-seq数据分析例子： http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/

• http://biow.sb-roscoff.fr/ecolebioinfo/trainingmaterial/chip-seq/documents/presentation_chipseq.pdf

• http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/chipseqCarlHerrmannRoscoff2015.pdf

• http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/defrance-ChIP-seq_annotation.pdf

然后下面的各种资料，是针对ChIP-seq流程的各个环境的，还有一些是针对于表观遗传学知识

• ppt : http://159.149.160.51/epigenmilano/epigenbarozzi.pdf

• best practise: http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/

• pipeline : https://github.com/shenlab-sinai/chip-seq_preprocess

• https://sites.google.com/site/anshul...e/projects/idr ## samtools view -b -F 1548 -q 30 chipSampleRep1.bam

• pipeline : http://daudin.icmb.utexas.edu/wiki/index.php/ChIPseqprepand_map

• pipeline : https://github.com/BradyLab/ChipSeq/blob/master/chipseq.sh

• https://github.com/crukci-bioinformatics/chipseq-pipeline

• https://github.com/ENCODE-DCC/chip-seq-pipeline

• Hands-on introduction to ChIP-seq analysis - VIB Training http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/

• video(A Step-by-Step Guide to ChIP-Seq Data Analysis Webinar) : http://www.abcam.com/webinars/a-step-by-step-guide-to-chip-seq-data-analysis-webinar

• Using ChIP-Seq to identify and/or quantify bound regions (peaks)http://barcwiki.wi.mit.edu/wiki/SOPs/chipseqpeaks

• http://jura.wi.mit.edu/bio/education/hottopics/ChIPseq/ChIPSeqHotTopics.pdf

• http://pedagogix-tagc.univ-mrs.fr/courses/ASG1/practicals/chip-seq/mapping_tutorial.html

• 公开课： https://www.coursera.org/learn/galaxy-project/lecture/FUzcg/chip-sequence-analysis-with-macs

• EBI的教程：https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/chip-seq-analysis/chip-seq-practical

• 台湾教程：http://lsl.sinica.edu.tw/Services/Class/files/20151118475_2.pdf 徐唯哲 Paul Wei-Che HSU

• peak finder软件大全： http://wodaklab.org/nextgen/data/peakfinders.html

• https://www.encodeproject.org/documents/049704a4-5c58-4631-acf1-4ef152bdb3ef/@@download/attachment/LearningChromatinStatesfromChIP-seq_data.pdf

• https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/47aq5pp5mzza5vb/PDFs/TuesdayMBChIP-Seq_Intro.pdf

• paper： Large-Scale Quality Analysis of Published ChIP-seq Data http://www.g3journal.org/content/4/2/209.full

• paper： ChIp-seq data analysis: from quality check to motif discovery and more http://ccg.vital-it.ch/var/sibapril15/cases/landt12/strandcorrelation.html

• Workshop hands on session(RNA-Seq / ChIP-Seq ) : https://hpc.oit.uci.edu/biolinux/handson.docx

• http://www.gqinnovationcenter.com/documents/bioinformatics/ChIPseq.pptx

• paper supplement : http://genome.cshlp.org/content/suppl/2015/10/02/gr.192005.115.DC1/Supplemental_Information.docx

• http://www.illumina.com/documents/products/datasheets/datasheetchipsequence.pdf

• http://www.ncbi.nlm.nih.gov/pubmed/22130887 "Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization."

• http://www.ncbi.nlm.nih.gov/pubmed/22499706 "Normalization, bias correction, and peak calling for ChIP-seq." (stat heavy)

• http://www.ncbi.nlm.nih.gov/pubmed/24244136 "Practical guidelines for the comprehensive analysis of ChIP-seq data."

• http://www.ncbi.nlm.nih.gov/pubmed/25223782 "Identifying and mitigating bias in next-generation sequencing methods for chromatin biology."

• http://www.ncbi.nlm.nih.gov/pubmed/24598259 "Impact of sequencing depth in ChIP-seq experiments."

• figures: https://github.com/shenlab-sinai/ngsplot

• https://github.com/daler/metaseq

• http://liulab.dfci.harvard.edu/CEAS/usermanual.html

• http://faculty.ucr.edu/~tgirke/HTMLPresentations/Manuals/WorkshopDec610_2012/Rchipseq/Rchipseq.pdf

• http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day4/chipqc_sweave.pdf

• http://bioconductor.org/packages/release/bioc/html/chipseq.html

• http://bioconductor.org/help/workflows/chipseqDB/

• http://bioconductor.org/help/workflows/generegulation/

• http://bioconductor.org/help/course-materials/2009/EMBLJune09/Practicals/chipseq/BasicChipSeq.pdf

• http://www.partek.com/Tutorials/microarray/Tiling/ChipSeqTutorial.pdf