美文网首页NGS基因组
#GTF/GFF格式# gffread入门使用

#GTF/GFF格式# gffread入门使用

作者: 土豆_leah | 来源:发表于2018-10-10 11:55 被阅读767次

    首先了解一下GTF/GFF的格式
    https://asia.ensembl.org/info/website/upload/gff.html
    两者的关系如下

    GTF (gene transfer format) is identical to GFF (general feature format) version 2

    • GFF格式主要是用来注释基因组
    • GTF主要是用来对基因进行注释,比如基因在染色体上的位置(coordinate)及这段区间的其他信息。
      两者在内容上前八列相同,最后一列信息显示不一致,gff文件格式如下:
    1. seqid - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seq ID must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below. (id,一般为chr或者scanfold编号)
    2. source - name of the program that generated this feature, or the data source (database or project name) (注释的来源,如果未知用.代替)
    3. type - type of feature. Must be a term or accession from the SOFA sequence ontology (注释信息的类型,比如Gene、cDNA、mRNA、CDS等)
    4. start - Start position of the feature, with sequence numbering starting at 1.
    5. end - End position of the feature, with sequence numbering starting at 1.
    6. score - A floating point value. (序列相似性比对时的E-values值或者基因预测是的P-values值,“.”表示为空)
    7. strand - defined as + (forward) or - (reverse).(正反义链)
    8. phase - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on. (CDS类型中指出该值,值为CDS的起始位置,除以3得到的余数)
    9. attributes - A semicolon-separated list of tag-value pairs, providing additional information about each feature. Some of these tags are predefined, e.g. ID, Name, Alias, Parent - see the GFF documentation for more details. (以多个键值对组成的注释信息描述,键与值之间用“=”,不同的键值用“;)

    安装如下:

      cd /some/build/dir
      git clone https://github.com/gpertea/gclib
      git clone https://github.com/gpertea/gffread
      cd gffread
      make
    

    程序是c++编写的因此并不需要预装一些包,当然也可以使用conda安装。

    conda install gffread -y
    

    使用的例子如下:

    #下载gtf/gff文档及hg19文件
    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
    wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz
    wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
    #使用gunzip及tar分别解压,并合并下载内容获得hg19.fa
    cat *.fa >hg19.fa
    #根据hg19.fa提取CDS序列
    gffread gencode.v19.annotation.gff3 -g hg19.fa -y tr_cds.fa
    #翻译后蛋白序列
    gffread gencode.v19.annotation.gff3 -g hg19.fa -x cds.fa
    #获得外显子序列
    gffread gencode.v19.annotation.gff3 -g hg19.fa -w exons.fa
    #格式转换
    gffread gencode.v19.annotation.gff3 -T -o gencode.v19.gtf
    gffread merged.gtf -o- > merged.gff3
    

    程序非常简约,通过man gffread查看使用说明
    github地址 https://github.com/gpertea/gffread

    相关文章

      网友评论

        本文标题:#GTF/GFF格式# gffread入门使用

        本文链接:https://www.haomeiwen.com/subject/xaxpaftx.html