Error for Gencode gtf #180
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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?
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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Here is an extracted part of all needed lines - all needed features (gene, transcript, exon) are present
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)
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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";
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Brian J. Haas
The Broad Institute
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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.fastaAnd 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?
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