https://divingintogeneticsandgenomics.com/tags/histone-modifications/ Recent content in Histone modifications on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 20 Apr 2017 18:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/several-very-interesting-histone-modification-epigenetics-papers/ Thu, 20 Apr 2017 18:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/several-very-interesting-histone-modification-epigenetics-papers/ If you have read my previous post Misconcept of epigenetics , you will know that: histone modification is not epigenetics! However, recently, four papers in Science actually showed that histone modifications actually have a component of inheritance: Causal role for inheritance of H3K27me3 in maintaining the OFF state of a *Drosophila* HOX gene DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA https://divingintogeneticsandgenomics.com/archive/chip-seq-analysis-part1/ Tue, 23 Jun 2015 12:30:00 -0700 https://divingintogeneticsandgenomics.com/archive/chip-seq-analysis-part1/ sofware installation and data source install MACS2: 06/11/2015 sudo pip -H install MACS2 macs2 version:2.1.0.20150420 install NCIS to estimate the scaling factor: Download the package here: wget http://www.biomedcentral.com/content/supplementary/1471-2105-13-199-s2.gz It is a .gz file, you can open your Rstudio and install it: install.packages("~/NCIS/1471-2105-13-199-s2.gz", repos = NULL, type="source") For help: library(NCIS); ?NCIS see a post here using NCIS before MACS peak calling: Adding a custom normalization to MACS. when use NCIS, one needs to deduplicate the reads first.