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This article mainly explains "how to install Juicer software". Interested friends may wish to have a look at it. The method introduced in this paper is simple, fast and practical. Now let the editor take you to learn "the installation method of Juicer software"!

Software installation is one of the most basic skills in bioinformatics practice. Only by ensuring that the software is installed correctly will it be easy to use later, and there will not be a lot of bug. Juicer software provides pipeline for one-click analysis of Hi-C data, which makes it easier for users to operate. Of course, when the analysis ability is strong, the more software it depends on, and the more complex the installation process will be. This paper mainly records the installation process of the software, which can be divided into the following steps.

1. Install dependent softwar

The core of juicer is developed in java language with scaffolding scripts developed by perl, python, bash and so on. Bwa software is used in sequence alignment, while samtools software is used in the bam files generated by subsequent operations. So you need to install the following software

Java

Perl

Python

GNU utils

Bwa

Samtools

These software are the basic software in the field of Shengxin, and the installation process will not be carried out in detail.

two。 Establish a directory structure

Juicer software requires a fixed directory structure. Create a new directory called juicer, which is the installation directory of the software. There must be the following four subdirectories under this directory.

The references directory is used to store reference genome related files, work is used to store sample sequence files and analysis results, scripts is used to store scripts needed for software operation, and restriction_sites is used to store reference genome restriction endonuclease maps.

3. Download the juicer source code

Download the source code for juicer and jcuda from github and place it in the scripts directory. Juicer can be run on a stand-alone or cluster system, and its intermediate scripts also correspond to different systems, as shown below

The CPU directory is a stand-alone server, while AWS, LSF, PBS, etc., correspond to public clouds and different cluster systems. Take CPU as an example, the download process is as follows

# download source code

Git clone https://github.com/aidenlab/juicer.git

# rename to scripts directory

Ln-s juicer/CPU scripts

Cd scripts/common

Wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar

Ln-s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar4. Prepare the reference genome document

The reference genome-related files in the reference directory are actually the corresponding fasta sequence files and bwa indexes, as shown below

Hg19.fasta

Hg19.fasta.sa

Hg19.fasta.ann

Hg19.fasta.amb

Hg19.fasta.pac

Hg19.fasta.bwt

Download genomic fasta files from databases such as UCSC,NCBI according to your needs and index them with bwa.

Refer to the restriction endonuclease map of the genome in the restriction_sites directory, which can be generated through the built-in generate_site_positions.py script in jucier. The script is located in the misc directory in the source code and supports the direct output of the following four endonucleases.

HindIII

DpnII

MboI

Sau3AI

The usage is as follows

Generate_site_positions.py HindIII hg19 hg19.fasta

The first parameter is the name of the endonuclease, the second parameter is the custom genome version, and the third parameter is the path of the genome fasta file. The name of the output file is the second parameter and the first parameter is linked with an underscore with the suffix txt. The output file of the above code is

Hg19_HindIII.txt

5. Prepare the fastq sequence of the sample

After performing the first four steps, the software has been installed. When the software runs, it also has a requirement for the location of the sample files. It must be located in the work directory, with the sample name as a subdirectory, and the sequence files are stored in the fastq directory, as shown below.

/ opt/juicer/work/MBR19/fastq

/ opt/juicer/work/MBR19/fastq/chr19_R1.fastq.gz

/ opt/juicer/work/MBR19/fastq/chr19_R2.fastq.gz

For the directory structure after successful installation, you can refer to the following link

Https://bcm.app.box.com/v/juicerawsmirror/folder/11284128669

The installation process of juicer is not complicated, but there are many matters needing attention, and it is more tedious to operate. If you only need to follow the above steps patiently, you can install successfully quickly.

At this point, I believe that you have a deeper understanding of the "installation method of Juicer software", you might as well come to the actual operation! Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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