FastQC的安装与使用

FastQC的安装与使用

本文作者：Sunny-King

发布时间：2022-06-09

本文链接：https://www.cnblogs.com/Sunny-King/p/Bioinformatics-FastQC.html

一、下载安装

1、准备工作---java环境

FastQC是一个java应用程序。为了运行它，需要您的系统安装合适的Java运行时环境。因此，在尝试运行FastQC之前，应该确保有一个合适的Java运行时环境。

$ java -version
openjdk version "1.8.0_192"
OpenJDK Runtime Environment (Zulu 8.33.0.1-linux64) (build 1.8.0_192-b01)
OpenJDK 64-Bit Server VM (Zulu 8.33.0.1-linux64) (build 25.192-b01, mixed mode)

2、下载FastQC

FastQC提供编译好的文件，下载后可以直接运行。也可以自己下载源代码自行编译。从网页获取下载链接，利用wget下载编译好的文件，目前最新的是v0.11.9版本。

下载网址：https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

# 下载
wget --no-check-certificate https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
# 解压
unzip fastqc_v0.11.9.zip

# 添加可执行权限
cd FastQC
chmod +x fastqc

3、Conda安装

直接使用conda安装

conda install fastqc

二、软件参数和使用

1、常用的参数设置

• -h|--help: 输出帮助信息
• -o|--outdir：输出结果路径
• -t|--threads： 使用线程个数
• --extract：输出结果解压缩。
• -a|--adapters：自己指定的adapter序列。默认的序列是Illumina的接头序列，可以在FastQC/Configuration/adapter_list.txt文件中获取。

2、使用示例

$ fastqc -o ./ -t 1 Sample.R1.fastq.gz 
$ ls
Sample.R1.fastq.gz Sample.R1.fastqc.zip Sample.R1.fastqc.html 

下载html到本地可以用浏览器打开即可看到质控分析结果。

如果在流程中可以从Sample.R1.fastqc/fastqc_data.txt文件中读取数据。

同时输出的html的报告支持修改格式，可以替换为自己的模板。修改安装路径下的FastQC/Templates/header_template.html文件即可输出自己想要的风格。

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附表：FastQC参数信息

点击查看代码

$ fastqc -h
            FastQC - A high throughput sequence QC analysis tool

SYNOPSIS

	fastqc seqfile1 seqfile2 .. seqfileN

    fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam][-c contaminant file] seqfile1 .. seqfileN

DESCRIPTION

    FastQC reads a set of sequence files and produces from each one a quality control report consisting of a number of different modules, each one of which will help to identify a different potential type of problem in your data.
    If no files to process are specified on the command line then the program will start as an interactive graphical application.  If files are provided on the command line then the program will run with no user interaction required.  In this mode it is suitable for inclusion into a standardised analysis pipeline.
    The options for the program as as follows:
    -h --help       Print this help file and exit
    -v --version    Print the version of the program and exit
    -o --outdir     Create all output files in the specified output directory.
                    Please note that this directory must exist as the program
                    will not create it.  If this option is not set then the 
                    output file for each sequence file is created in the same
                    directory as the sequence file which was processed.
    --casava        Files come from raw casava output. Files in the same sample
                    group (differing only by the group number) will be analysed
                    as a set rather than individually. Sequences with the filter
                    flag set in the header will be excluded from the analysis.
                    Files must have the same names given to them by casava
                    (including being gzipped and ending with .gz) otherwise they
                    won't be grouped together correctly.
    --nano          Files come from nanopore sequences and are in fast5 format. In
                    this mode you can pass in directories to process and the program
                    will take in all fast5 files within those directories and produce
                    a single output file from the sequences found in all files.
    --nofilter      If running with --casava then don't remove read flagged by
                    casava as poor quality when performing the QC analysis.
    --extract       If set then the zipped output file will be uncompressed in
                    the same directory after it has been created.  By default
                    this option will be set if fastqc is run in non-interactive
                    mode.
    -j --java       Provides the full path to the java binary you want to use to
                    launch fastqc. If not supplied then java is assumed to be in
                    your path.
    --noextract     Do not uncompress the output file after creating it.  You
                    should set this option if you do not wish to uncompress
                    the output when running in non-interactive mode.
    --nogroup       Disable grouping of bases for reads >50bp. All reports will
                    show data for every base in the read.  WARNING: Using this
                    option will cause fastqc to crash and burn if you use it on
                    really long reads, and your plots may end up a ridiculous size.
                    You have been warned!
    --min_length    Sets an artificial lower limit on the length of the sequence
                    to be shown in the report.  As long as you set this to a value
                    greater or equal to your longest read length then this will be
                    the sequence length used to create your read groups.  This can
                    be useful for making directly comaparable statistics from datasets with somewhat variable read lengths.
    -f --format     Bypasses the normal sequence file format detection and
                    forces the program to use the specified format.  Valid
                    formats are bam,sam,bam_mapped,sam_mapped and fastq
    -t --threads    Specifies the number of files which can be processed
                    simultaneously.  Each thread will be allocated 250MB of
                    memory so you shouldn't run more threads than your
                    available memory will cope with, and not more than
                    6 threads on a 32 bit machine
    -c --contaminants Specifies a non-default file which contains the list of
                    contaminants to screen overrepresented sequences against.
                    The file must contain sets of named contaminants in the
                    form name[tab]sequence.  Lines prefixed with a hash will
                    be ignored.
    -a --adapters   Specifies a non-default file which contains the list of
                    adapter sequences which will be explicity searched against
                    the library. The file must contain sets of named adapters
                    in the form name[tab]sequence.  Lines prefixed with a hash
                    will be ignored.
    -l --limits     Specifies a non-default file which contains a set of criteria
                    which will be used to determine the warn/error limits for the
                    various modules.  This file can also be used to selectively 
                    remove some modules from the output all together.  The format
                    needs to mirror the default limits.txt file found in the
                    Configuration folder.
   -k --kmers       Specifies the length of Kmer to look for in the Kmer content
                    module. Specified Kmer length must be between 2 and 10. Default
                    length is 7 if not specified.
   -q --quiet       Supress all progress messages on stdout and only report errors.
   -d --dir         Selects a directory to be used for temporary files written when
                    generating report images. Defaults to system temp directory if
                    not specified.
BUGS

    Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
    or in www.bioinformatics.babraham.ac.uk/bugzilla/