GRCh38基因组和注释文件探究
ensembl/release91:
cat Homo_sapiens.GRCh38.91.gtf | grep -v "#" | cut -f9 | cut -f1,3,6,8 -d\; | grep gene_biotype | sed -e 's/\"//g' | sed -e 's/\;//g' | cut -f2,6,8 -d" " | sort | uniq > GRCh38.feature.info
ENSG00000000003 TSPAN6 protein_coding
ENSG00000000005 TNMD protein_coding
ENSG00000000419 DPM1 protein_coding
ENSG00000000457 SCYL3 protein_coding
ENSG00000000460 C1orf112 protein_coding
ENSG00000000938 FGR protein_coding
ENSG00000000971 CFH protein_coding
ENSG00000001036 FUCA2 protein_coding
ENSG00000001084 GCLC protein_coding
ENSG00000001167 NFYA protein_coding
ENSG00000001460 STPG1 protein_coding
ENSG00000001461 NIPAL3 protein_coding
ENSG00000001497 LAS1L protein_coding
ENSG00000001561 ENPP4 protein_coding
ENSG00000001617 SEMA3F protein_coding
ENSG00000001626 CFTR protein_coding
ENSG00000001629 ANKIB1 protein_coding
ENSG00000001630 CYP51A1 protein_coding
ENSG00000001631 KRIT1 protein_coding
ENSG00000002016 RAD52 protein_coding
ENSG00000002079 MYH16 transcribed_unitary_pseudogene
ENSG00000002330 BAD protein_coding
ENSG00000002549 LAP3 protein_coding
ENSG00000002586 CD99 protein_coding
ENSG00000002587 HS3ST1 protein_coding
ENSG00000002726 AOC1 protein_coding
ENSG00000002745 WNT16 protein_coding
ENSG00000002746 HECW1 protein_coding
ENSG00000002822 MAD1L1 protein_coding
ENSG00000002834 LASP1 protein_coding
ENSG00000002919 SNX11 protein_coding
ENSG00000002933 TMEM176A protein_coding
ENSG00000003056 M6PR protein_coding
ENSG00000003096 KLHL13 protein_coding
ENSG00000003137 CYP26B1 protein_coding
58302个ENSG id
56655个gene name（为什么有将近两千个是重复）
46种类型：
31 3prime_overlapping_ncRNA
5517 antisense_RNA
19 bidirectional_promoter_lncRNA
14 IG_C_gene
9 IG_C_pseudogene
37 IG_D_gene
18 IG_J_gene
3 IG_J_pseudogene
1 IG_pseudogene
144 IG_V_gene
188 IG_V_pseudogene
7493 lincRNA
1 macro_lncRNA
1879 miRNA
2221 misc_RNA
2 Mt_rRNA
22 Mt_tRNA
3 non_coding
63 polymorphic_pseudogene
10235 processed_pseudogene
543 processed_transcript
19847 protein_coding
22 pseudogene
8 ribozyme
549 rRNA
49 scaRNA
1 scRNA
904 sense_intronic
189 sense_overlapping
943 snoRNA
1909 snRNA
5 sRNA
1066 TEC
462 transcribed_processed_pseudogene
111 transcribed_unitary_pseudogene
828 transcribed_unprocessed_pseudogene
2 translated_processed_pseudogene
6 TR_C_gene
4 TR_D_gene
79 TR_J_gene
4 TR_J_pseudogene
108 TR_V_gene
30 TR_V_pseudogene
95 unitary_pseudogene
2637 unprocessed_pseudogene
1 vaultRNA
GENCODE的注释gtf文件：
##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74)
##provider: GENCODE
##contact: gencode@sanger.ac.uk
##format: gtf
##date: 2013-12-05
chr1 HAVANA gene 11869 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN";gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
ensembl
#!genome-build GRCh38.p10
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.25
#!genebuild-last-updated 2017-06
1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
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"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype"processed_transcript"; tag "basic"; transcript_support_level "1";
1 havana exon 11869 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 12613 12721 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana transcript 12010 13670 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype"transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
问题：
1. 为什么用gencode的注释文件做表达定量会出问题？
2. 不同的release之间有什么区别？
3. 不同来源的注释区别在哪里？
4.
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