[Dowen_Fan]

[ChIA-PET data processing and Insulated neighborhood building pipeline]
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Quick Start

Installing Dowen_Fan:

git clone https://github.com/stjude/Dowen_Fan.git; cd Dowen_Fan

Description:

Dowen_Fan is a pipeline that enables user to define significantly interacting ChIA-PET loops. This tool is robust and efficient in deducing the Insulated Neighborhoods.

Dependencies

cutadapt (v 4.3)
macs14 (v 1.4.2)
bowtie (v 2.3.5.1)
samtools (v 1.15.1)
bedtools (v 2.30.0)
Python
R (v 4.2.2)

Usage

sh singlenodeChIA-PETv5.sh -f file_R1.fastq -r file_R2.fastq -b fullpath_bowtieindexname

where:

f1 is forward fastq read file from ChIA-PET

r1 is reverse fastq read file from ChIA-PET

b is full path including the index name (bowtie indexed genome)

Contact

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Limitations

Are there any know limits to the tool. Some examples of this might be:

• Does not run on OSX
• Version 1.2 of library XYZ causes this unexpected behavior

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COPYRIGHT

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