初步了解hg19注释文件的内容 | gtf

hg19有哪些染色体？

chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM

其实还有其他“染色体”，只是我们的研究一般用不到，所以就没有合并进来。比如做同源分析，找变异什么的，还是要选好基因组。

gene_type有哪些？

cat gencode.v27.annotation.gtf | grep exon | cut -f6 -d\" | grep -v "#" | sort | uniq > gene_type

3prime_overlapping_ncRNA
IG_C_gene
IG_C_pseudogene
IG_D_gene
IG_J_gene
IG_J_pseudogene
IG_V_gene
IG_V_pseudogene
IG_pseudogene
MIAT_exon1
MIAT_exon5_1
MIAT_exon5_2
MIAT_exon5_3
Mt_rRNA
Mt_tRNA
SOX2OT_exon1
SOX2OT_exon3
SOX2OT_exon4
TEC
TR_C_gene
TR_D_gene
TR_J_gene
TR_J_pseudogene
TR_V_gene
TR_V_pseudogene
Xist_exon1
Xist_exon4
antisense_RNA
bidirectional_promoter_lncRNA
lincRNA
macro_lncRNA
miRNA
misc_RNA
non_coding
polymorphic_pseudogene
processed_pseudogene
processed_transcript
protein_coding
pseudogene
rRNA
ribozyme
sRNA
scRNA
scaRNA
sense_intronic
sense_overlapping
snRNA
snoRNA
transcribed_processed_pseudogene
transcribed_unitary_pseudogene
transcribed_unprocessed_pseudogene
translated_processed_pseudogene
unitary_pseudogene
unprocessed_pseudogene
vaultRNA

一共多少个基因？

cat gencode.v27.annotation.gtf | cut -f4 -d\; |  grep -v "#" | grep -v level | sort | uniq > gene

56609　　

一共多少个转录本？

cat gencode.v27.annotation.gtf | cut -f2 -d\; |  grep -v "#" | grep -v gene_type | sort | uniq > transcipt

200401　　

一共多少个外显子？

cat gencode.v27.annotation.gtf | grep -v "#" | grep exon | cut -f3-5 | sort | uniq > exon

1132357　　

有多少条lncRNA

cat gencode.v27.long_noncoding_RNAs.gtf | grep -v "#" | cut -f3 -d\; | grep -v gene_type | sort | uniq > lincRNA

15754