<![CDATA[chip-seq]]>1.chipseq介绍
https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html
0ab4f3f3-aace-4fbb-9079-4ae4d7928020-image.png

28a1c03f-2afa-4bb3-853c-bd8bee2900b3-image.png

https://angus.readthedocs.io/en/2019/chip-seq.html
2ea61161-668e-409c-bb82-ab8a9f248d77-image.png

]]>http://an.forum.genostack.com/topic/748/chip-seqRSS for NodeSat, 13 Jun 2026 12:35:36 GMTMon, 08 Aug 2022 03:58:02 GMT60<![CDATA[Reply to chip-seq on Wed, 10 Aug 2022 06:53:55 GMT]]>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828144/
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
3d1f0fc6-d2ed-4539-9cde-0c03bde51949-image.png

]]>http://an.forum.genostack.com/post/1785http://an.forum.genostack.com/post/1785Wed, 10 Aug 2022 06:53:55 GMT<![CDATA[Reply to chip-seq on Wed, 17 Aug 2022 12:37:01 GMT]]>(Focus computational biology series) Bardet, Anaïs F._ Mifsud, Borbala_ Zarnack, Katharina - Practical guide to ChIP-seq_ data analysis-CRC Press (2019).pdf

本书附件
https://anaisbardet.cnrs.fr/practical-guide-to-chip-seq-data-analysis/

documents-export-2022-08-17.zip

]]>http://an.forum.genostack.com/post/1783http://an.forum.genostack.com/post/1783Wed, 17 Aug 2022 12:37:01 GMT<![CDATA[Reply to chip-seq on Tue, 09 Aug 2022 08:35:24 GMT]]>测试数据：
https://www.sciencedirect.com/science/article/pii/S009286740800617X

该测试省略了质控QC 步骤 参考七桥的过程 把QC和去重也加上。
1.构建参考基因组索引
系统要内置人类和鼠的参考基因组

bowtie2-build mm10.fa mm10

2.比对
chip-seq通常有个对照样本 但是这个对照样本是可选的 我们在流程中设定为可选步骤

bowtie2 -x mm10 -U SRR002012_Oct4.fastq -S Oct4.sam -p 6
samtools sort Oct4.sam -O Oct4_sorted.bam
bowtie2 -x mm10 -U SRR001996_GFP_Control.fastq -S GFP.sam -p 6
samtools sort GFP.sam -o GFP_sorted.bam

3.call peak
name、gsize、tsize暴露为参数

macs2 callpeak -t Oct4_sorted.bam -c GFP_sorted.bam --format=BAM --name=Oct4 --gsize=138000000 --tsize=26

该流程的结果可视化 可以直接使用IGV 查看bed文件

]]>http://an.forum.genostack.com/post/1782http://an.forum.genostack.com/post/1782Tue, 09 Aug 2022 08:35:24 GMT