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This article mainly explains "how to use phantompeakqualtools for cross correlation analysis". Interested friends may wish to take a look. The method introduced in this paper is simple, fast and practical. Let's take you to learn "how to use phantompeakqualtools for cross correlation analysis"!

ENCODE officially provides the pipeline of chip_seq analysis for reference. In the pre-processing link before peak calling, the flow diagram is as follows

You can see that it contains a tool called phantompeakqualtools, which can perform cross-correlation analysis and calculate the two index values NSC and RSC. The source code of the software is saved on github. The website is as follows

https://github.com/kundajelab/phantompeakqualtools

The installation process is as follows

docker run -it -v /home:/home --rm centos

yum install -y epel-release

yum install -y R

yum install -y wget

yum install -y ncurses-devel bzip2 libcurl libcurl-devel

# samtools

wget https://sourceforge.net/projects/samtools/files/samtools/1.9/samtools-1.9.tar.bz2

tar xjvf samtools-1.9.tar.bz2

cd samtools-1.9

./ configure

make

make install

# R

install.packages("BiocManager")

BiocManager::install("Rsamtools", version = "3.8")

install.packages("spp")

install.packages("snow")

install.packages("snowfall")

# phantompeakqualtools

wget https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz

tar xzvf 1.2.tar.gz

The basic usage is as follows

Rscript run_spp.R \

-c=chip.bam \

-rf -p=10 \

-filtchr="chrM" \

-savp=cc.plot.pdf \

-out=cc.score.txt

The software runs for a long time, pdf results are shown below

Blue marks are the positions of phantom peaks. In the txt output file, each column represents an indicator, but there is no header, which can be understood by referring to the log information output to the screen, as follows

Minimum cross-correlation value 0.3735286

Minimum cross-correlation shift 1500

Top 3 cross-correlation values 0.412562930952545,0.37885721605778,0.375020285168966

Top 3 estimates for fragment length 150,285,525

Window half size 200

Phantom peak location 95

Phantom peak Correlation 0.3845194

Normalized Strand cross-correlation coefficient (NSC) 1.104502

Relative Strand cross-correlation Coefficient (RSC) 3.551565

Phantom Peak Quality Tag 2 At this point, I believe that everyone has a deeper understanding of "how to use phantompeakqualtools for cross correlation analysis", so let's actually operate it! Here is the website, more related content can enter the relevant channels for inquiry, pay attention to us, continue to learn!

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