Error for Gencode gtf #180

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1. brianjohnhaas commented on Aug 22, 2023

   

   brianjohnhaas

   on Aug 22, 2023 via email

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   not sure. You could try to grep 'ENST00000456328.2' from the gencode gtf and see if there's a 'gene' feature corresponding to it.

   …

   On Tue, Aug 22, 2023 at 12:57 PM taigalokhid ***@***.***> wrote: Hi Brian, I try to create a transcripts.fasta for decoy chromosomes and virus chromosomes. I run util/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta And on a Gencode gtf it gave me an Error with duplicated tags After this I try to realize gff3 -> bed12 -> fasta from bedtools I try to run gff3_file_to_bed.pl on a Gencode gff3 And I receive Error, no gene feature found for ENST00000456328.2.... ignoring feature. Could you clarify, what is the problem with features in Genecode gtf? — Reply to this email directly, view it on GitHub <#180>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX475APZV3WQOEDKOV3XWTQIPANCNFSM6AAAAAA32G7E3M> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
2. taigalokhid commented on Aug 22, 2023

   

   taigalokhid

   on Aug 22, 2023

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   Here is an extracted part of all needed lines - all needed features (gene, transcript, exon) are present

   chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000290825.1"; gene_type "lncRNA"; gene_name "DDX11L2"; level 2; tag "overlaps_pseudogene";
   chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA gene 12010 13670 . + . gene_id "ENSG00000223972.6"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; hgnc_id "HGNC:37102"; havana_gene "OTTHUMG00000000961.2";

   I grep it - Gene_id exist and in the same format as gtf for stringtie result (https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual)

   sharova@tux:/data7a/bio/human_genomics/shared/maps/GDC.h38.d1.vd1/gencodev43$ grep 'ENST00000456328.2' gencode.v43.chr_patch_hapl_scaff.annotation.100.gtf

   chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
   chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1";
3. brianjohnhaas commented on Aug 23, 2023

   

   brianjohnhaas

   on Aug 23, 2023 via email

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   Great. If you now grep the gene_id "ENSG00000290825.1", does it show a 'gene' feature type?

   …

   On Tue, Aug 22, 2023 at 5:15 PM taigalokhid ***@***.***> wrote: ***@***.***:/data7a/bio/human_genomics/shared/maps/GDC.h38.d1.vd1/gencodev43$ grep 'ENST00000456328.2' gencode.v43.chr_patch_hapl_scaff.annotation.100.gtf chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1"; chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1"; chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1"; chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_transcript "OTTHUMT00000362751.1"; — Reply to this email directly, view it on GitHub <#180 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2XQV2NJWN4MHIMU23XWUOP3ANCNFSM6AAAAAA32G7E3M> . You are receiving this because you commented.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>