I have just started using HTSeq and found problems using GFF file. I have checked some of the threads in seqanswers but couldn't fix.
Here is the command and error:
htseq-count sorted.sam ../ref_CanFam3.1_top_level.gff3
Error occured in line 9 of file ../ref_CanFam3.1_top_level.gff3.
Error: Feature id1 does not contain a 'gene_id' attribute
[Exception type: SystemExit, raised in count.py:55]
Below are a few lines of my GFF file:
#gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region chr1 1 122678785
##species http://www.ncbi.nlm.nih.gov/Taxonomy...ax.cgi?id=9615
chr1 RefSeq region 1 122678785 . + . ID=id0;Name=1;Dbxref=taxon:9615;breed=boxer;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA;sex=female;sub-species=familiaris
chr1 Gnomon gene 251990 322081 . - . ID=gene0;Name=ENPP1;Dbxref=GeneID:100856150;gbkey=Gene;gene=ENPP1;part=1%2F1
chr1 Gnomon mRNA 251990 322081 . - . ID=rna0;Name=XM_003638785.2;Parent=gene0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 321851 322081 . - . ID=id1;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 289674 289746 . - . ID=id2;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 287787 287903 . - . ID=id3;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 286842 286967 . - . ID=id4;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 285904 285964 . - . ID=id5;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
Could someone help to fix this?
Here is the command and error:
htseq-count sorted.sam ../ref_CanFam3.1_top_level.gff3
Error occured in line 9 of file ../ref_CanFam3.1_top_level.gff3.
Error: Feature id1 does not contain a 'gene_id' attribute
[Exception type: SystemExit, raised in count.py:55]
Below are a few lines of my GFF file:
#gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region chr1 1 122678785
##species http://www.ncbi.nlm.nih.gov/Taxonomy...ax.cgi?id=9615
chr1 RefSeq region 1 122678785 . + . ID=id0;Name=1;Dbxref=taxon:9615;breed=boxer;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA;sex=female;sub-species=familiaris
chr1 Gnomon gene 251990 322081 . - . ID=gene0;Name=ENPP1;Dbxref=GeneID:100856150;gbkey=Gene;gene=ENPP1;part=1%2F1
chr1 Gnomon mRNA 251990 322081 . - . ID=rna0;Name=XM_003638785.2;Parent=gene0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 321851 322081 . - . ID=id1;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 289674 289746 . - . ID=id2;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 287787 287903 . - . ID=id3;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 286842 286967 . - . ID=id4;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
chr1 Gnomon exon 285904 285964 . - . ID=id5;Parent=rna0;Dbxref=GeneID:100856150,Genbank:XM_003638785.2;gbkey=mRNA;gene=ENPP1;product=ectonucleotide pyrophosphatase%2Fphosphodiesterase 1;transcript_id=XM_003638785.2
Could someone help to fix this?
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