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？

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