探索gff/gtf格式

Posted 2020-08-31 Digital-LI

参考：

GFF格式说明

Generic Feature Format Version 3 (GFF3)

先下载一个 gtf 文件浏览一下

1       havana  gene    11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2";
1       havana  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1";

有一个 R 的版本，可以看一看：R的bioconductor包TxDb.Hsapiens.UCSC.hg19.knownGene详解

另外，看看 Bioconductor的数据包library(org.Hs.eg.db)简介，了解一些基本的常识。