text: user10386: I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this:
  ##description: evidence-based annotation of the human genome (GRCh38), version 41 (Ensembl 107) - polyA features
  ##provider: GENCODE
  ##contact: gencode-help@ebi.ac.uk
  ##format: gtf
  ##date: 2022-05-12
  chr1    HAVANA  pseudo_polyA    134957  134962  .   -   .   gene_id "383460"; transcript_id "383460"; gene_type "pseudo_polya"; gene_name "383460"; transcript_type "pseudo_polya"; transcript_name "383460"; level 2;
  chr1    HAVANA  polyA_site  141474  141475  .   -   .   gene_id "383461"; transcript_id "383461"; gene_type "polya_site"; gene_name "383461"; transcript_type "polya_site"; transcript_name "383461"; level 2;
  chr1    HAVANA  polyA_signal    141477  141482  .   -   .   gene_id "383462"; transcript_id "383462"; gene_type "polya_signal"; gene_name "383462"; transcript_type "polya_signal"; transcript_name "383462"; level 2;
  chr1    HAVANA  pseudo_polyA    184934  184939  .   -   .   gene_id "383463"; transcript_id "383463"; gene_type "pseudo_polya"; gene_name "383463"; transcript_type "pseudo_polya"; transcript_name "383463"; level 2;
  chr1    HAVANA  pseudo_polyA    258530  258535  .   -   .   gene_id "383464"; transcript_id "383464"; gene_type "pseudo_polya"; gene_name "383464"; transcript_type "pseudo_polya"; transcript_name "383464"; level 2;
  
  In this GTF file, what does the gene_id mean? In the whole genome GTF (same build) the gene_id is clearly the ENSEMBL gene_id:
  ##description: evidence-based annotation of the human genome (GRCh38), version 41 (Ensembl 107)
  ##provider: GENCODE
  ##contact: gencode-help@ebi.ac.uk
  ##format: gtf
  ##date: 2022-05-12
  chr1    HAVANA  gene    11869   14409   .   +   .   gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; hgnc_id "HGNC:37102"; havana_gene "OTTHUMG00000000961.2";
  chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
  chr1    HAVANA  exon    11869   12227   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
  chr1    HAVANA  exon    12613   12721   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
  chr1    HAVANA  exon    13221   14409   .   +   .   gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
  
  
  What I want to do eventually is to assign the PolyA sites to ENSEMBL gene_ids.
  
  user16146: According to the GENCODE ftp README file, the value of the 'gene_id', 'transcript_id', 'gene_name' and 'transcript name' fields corresponds to a random identifier. The polyA features are not directly associated to any gene or transcript when manually annotated by Havana.
  There is other file in the GENCODE release that includes links between polyA features and transcripts:
  https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.metadata.PolyA_feature.gz
  
  ENST00000485748.5       3232    3233    chr1    1496201 1496202 +       polya_site
  ENST00000485748.5       3211    3216    chr1    1496180 1496185 +       polya_signal
  ENST00000474481.1       3367    3368    chr1    1496201 1496202 +       polya_site
  ENST00000474481.1       3346    3351    chr1    1496180 1496185 +       polya_signal
  ENST00000308647.8       2114    2115    chr1    1496201 1496202 +       polya_site
  ENST00000308647.8       2093    2098    chr1    1496180 1496185 +       polya_signal
  
  
  22. gencode.vX.metadata.PolyA_feature.gz:
    Manually annotated polyA feature overlapping the transcript 3'-end.
    1 - transcript id
    2 - transcript-based start coordinate of the polyA feature
    3 - transcript-based end coordinate of the polyA feature
    4 - polyA feature chromosome
    5 - polyA feature start coordinate
    6 - polyA feature end coordinate
    7 - polyA feature strand
    8 - polyA feature type ("polyA_site", "polyA_signal", "pseudo_polyA")
  
  
original_text: 10386: <p>I have downloaded the Gencode PolyA feature annotation GTF <a href="https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.polyAs.gtf.gz" rel="nofollow noreferrer">here</a>. The first 10 lines are like this:</p>
  <pre><code>##description: evidence-based annotation of the human genome (GRCh38), version 41 (Ensembl 107) - polyA features
  ##provider: GENCODE
  ##contact: gencode-help@ebi.ac.uk
  ##format: gtf
  ##date: 2022-05-12
  chr1    HAVANA  pseudo_polyA    134957  134962  .   -   .   gene_id &quot;383460&quot;; transcript_id &quot;383460&quot;; gene_type &quot;pseudo_polya&quot;; gene_name &quot;383460&quot;; transcript_type &quot;pseudo_polya&quot;; transcript_name &quot;383460&quot;; level 2;
  chr1    HAVANA  polyA_site  141474  141475  .   -   .   gene_id &quot;383461&quot;; transcript_id &quot;383461&quot;; gene_type &quot;polya_site&quot;; gene_name &quot;383461&quot;; transcript_type &quot;polya_site&quot;; transcript_name &quot;383461&quot;; level 2;
  chr1    HAVANA  polyA_signal    141477  141482  .   -   .   gene_id &quot;383462&quot;; transcript_id &quot;383462&quot;; gene_type &quot;polya_signal&quot;; gene_name &quot;383462&quot;; transcript_type &quot;polya_signal&quot;; transcript_name &quot;383462&quot;; level 2;
  chr1    HAVANA  pseudo_polyA    184934  184939  .   -   .   gene_id &quot;383463&quot;; transcript_id &quot;383463&quot;; gene_type &quot;pseudo_polya&quot;; gene_name &quot;383463&quot;; transcript_type &quot;pseudo_polya&quot;; transcript_name &quot;383463&quot;; level 2;
  chr1    HAVANA  pseudo_polyA    258530  258535  .   -   .   gene_id &quot;383464&quot;; transcript_id &quot;383464&quot;; gene_type &quot;pseudo_polya&quot;; gene_name &quot;383464&quot;; transcript_type &quot;pseudo_polya&quot;; transcript_name &quot;383464&quot;; level 2;
  </code></pre>
  <p>In this GTF file, what does the <code>gene_id</code> mean? In the whole genome <a href="https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz" rel="nofollow noreferrer">GTF</a> (same build) the <code>gene_id</code> is clearly the ENSEMBL gene_id:</p>
  <pre><code>##description: evidence-based annotation of the human genome (GRCh38), version 41 (Ensembl 107)
  ##provider: GENCODE
  ##contact: gencode-help@ebi.ac.uk
  ##format: gtf
  ##date: 2022-05-12
  chr1    HAVANA  gene    11869   14409   .   +   .   gene_id &quot;ENSG00000223972.5&quot;; gene_type &quot;transcribed_unprocessed_pseudogene&quot;; gene_name &quot;DDX11L1&quot;; level 2; hgnc_id &quot;HGNC:37102&quot;; havana_gene &quot;OTTHUMG00000000961.2&quot;;
  chr1    HAVANA  transcript  11869   14409   .   +   .   gene_id &quot;ENSG00000223972.5&quot;; transcript_id &quot;ENST00000456328.2&quot;; gene_type &quot;transcribed_unprocessed_pseudogene&quot;; gene_name &quot;DDX11L1&quot;; transcript_type &quot;processed_transcript&quot;; transcript_name &quot;DDX11L1-202&quot;; level 2; transcript_support_level &quot;1&quot;; hgnc_id &quot;HGNC:37102&quot;; tag &quot;basic&quot;; havana_gene &quot;OTTHUMG00000000961.2&quot;; havana_transcript &quot;OTTHUMT00000362751.1&quot;;
  chr1    HAVANA  exon    11869   12227   .   +   .   gene_id &quot;ENSG00000223972.5&quot;; transcript_id &quot;ENST00000456328.2&quot;; gene_type &quot;transcribed_unprocessed_pseudogene&quot;; gene_name &quot;DDX11L1&quot;; transcript_type &quot;processed_transcript&quot;; transcript_name &quot;DDX11L1-202&quot;; exon_number 1; exon_id &quot;ENSE00002234944.1&quot;; level 2; transcript_support_level &quot;1&quot;; hgnc_id &quot;HGNC:37102&quot;; tag &quot;basic&quot;; havana_gene &quot;OTTHUMG00000000961.2&quot;; havana_transcript &quot;OTTHUMT00000362751.1&quot;;
  chr1    HAVANA  exon    12613   12721   .   +   .   gene_id &quot;ENSG00000223972.5&quot;; transcript_id &quot;ENST00000456328.2&quot;; gene_type &quot;transcribed_unprocessed_pseudogene&quot;; gene_name &quot;DDX11L1&quot;; transcript_type &quot;processed_transcript&quot;; transcript_name &quot;DDX11L1-202&quot;; exon_number 2; exon_id &quot;ENSE00003582793.1&quot;; level 2; transcript_support_level &quot;1&quot;; hgnc_id &quot;HGNC:37102&quot;; tag &quot;basic&quot;; havana_gene &quot;OTTHUMG00000000961.2&quot;; havana_transcript &quot;OTTHUMT00000362751.1&quot;;
  chr1    HAVANA  exon    13221   14409   .   +   .   gene_id &quot;ENSG00000223972.5&quot;; transcript_id &quot;ENST00000456328.2&quot;; gene_type &quot;transcribed_unprocessed_pseudogene&quot;; gene_name &quot;DDX11L1&quot;; transcript_type &quot;processed_transcript&quot;; transcript_name &quot;DDX11L1-202&quot;; exon_number 3; exon_id &quot;ENSE00002312635.1&quot;; level 2; transcript_support_level &quot;1&quot;; hgnc_id &quot;HGNC:37102&quot;; tag &quot;basic&quot;; havana_gene &quot;OTTHUMG00000000961.2&quot;; havana_transcript &quot;OTTHUMT00000362751.1&quot;;
  
  </code></pre>
  <p>What I want to do eventually is to assign the PolyA sites to ENSEMBL gene_ids.</p>
   16146: <p>According to the GENCODE ftp <a href="https://ftp.ebi.ac.uk/pub/databases/gencode/_README.TXT" rel="nofollow noreferrer">README</a> file, the value of the 'gene_id', 'transcript_id', 'gene_name' and 'transcript name' fields corresponds to a random identifier. The polyA features are not directly associated to any gene or transcript when manually annotated by Havana.</p>
  <p>There is other file in the GENCODE release that includes links between polyA features and transcripts:
  <a href="https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.metadata.PolyA_feature.gz" rel="nofollow noreferrer">https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.metadata.PolyA_feature.gz</a></p>
  <pre>
  ENST00000485748.5       3232    3233    chr1    1496201 1496202 +       polya_site
  ENST00000485748.5       3211    3216    chr1    1496180 1496185 +       polya_signal
  ENST00000474481.1       3367    3368    chr1    1496201 1496202 +       polya_site
  ENST00000474481.1       3346    3351    chr1    1496180 1496185 +       polya_signal
  ENST00000308647.8       2114    2115    chr1    1496201 1496202 +       polya_site
  ENST00000308647.8       2093    2098    chr1    1496180 1496185 +       polya_signal
  </pre>
  <pre>
  22. gencode.vX.metadata.PolyA_feature.gz:
    Manually annotated polyA feature overlapping the transcript 3'-end.
    1 - transcript id
    2 - transcript-based start coordinate of the polyA feature
    3 - transcript-based end coordinate of the polyA feature
    4 - polyA feature chromosome
    5 - polyA feature start coordinate
    6 - polyA feature end coordinate
    7 - polyA feature strand
    8 - polyA feature type ("polyA_site", "polyA_signal", "pseudo_polyA")
  </pre>
  