https://divingintogeneticsandgenomics.com/tags/macs/ Recent content in MACS on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Mon, 14 Sep 2015 08:07:00 -0700 https://divingintogeneticsandgenomics.com/archive/macs2-parallel-peak-calling/ Mon, 14 Sep 2015 08:07:00 -0700 https://divingintogeneticsandgenomics.com/archive/macs2-parallel-peak-calling/ I want to use MACS2 call ChIP-seq peaks for 10 samples(each with IP and input control) with 4 different set of parameters. That's a lot of commands to type! Luckily, linux tricks come to help. First, put the sample names (prefix) in to a file: ls -1 *bam | sort | sed -r 's/-[A-G]{1}-NC.sorted.bam//g' | sort | uniq > sample_name.txt A is IP. G is input control. the prefix could be anything that tags each experiment. 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. https://divingintogeneticsandgenomics.com/archive/macs-for-dnase-seq-data/ Tue, 27 May 2014 19:22:00 -0700 https://divingintogeneticsandgenomics.com/archive/macs-for-dnase-seq-data/ It has been a long time since I posted last time. I will be defending at the end of next month. So, I am busy with my thesis writing. Anyway, I do want to keep a note here for using MACS to identify Dnase-seq peaks. Although MACS was developed for ChIP-seq. It can also be used for Dnase-seq data. see a discussion here: https://groups.google.com/forum/#!topic/macs-announcement/D1ZlzIJMBB8 several responses from the author of MACS Tao Liu: https://divingintogeneticsandgenomics.com/archive/hosting-bigwig-by-dropbox-for-ucsc-visualization/ Tue, 18 Feb 2014 12:53:00 -0800 https://divingintogeneticsandgenomics.com/archive/hosting-bigwig-by-dropbox-for-ucsc-visualization/ First, you need to get an idea of what is a bigwig file: https://genome.ucsc.edu/goldenPath/help/bigWig.html It is the binary form of wig file and allows UCSC genome browser to fetch only the data in the current window. I usually get wig file by MACS1.4 peak calling ChIP-seq data. MACS2 now does not have the -w option any more. https://github.com/taoliu/MACS/ see a discussion in the google group: https://groups.google.com/forum/#!searchin/macs-announcement/bedgraph$20ucsc$20track/macs-announcement/LBhAtmC-Zho/uZuxU8ZaqdEJ MACS2 only creates a bedgraph file http://genome. https://divingintogeneticsandgenomics.com/archive/chip-exo-data-analysis/ Sat, 16 Nov 2013 07:58:00 -0800 https://divingintogeneticsandgenomics.com/archive/chip-exo-data-analysis/ Our neighboring lab just generated some ChIP-exo data, (if you do not know the technique, look at this paper http://www.ncbi.nlm.nih.gov/pubmed/23026909) and the company did some analysis but not what they want. The bedgraph files generated by the company were separated for plus strand and minus strand. They want just peak files like in the ChIP-seq experiment. I was aware of several software can be used to deal with this type of data: