Question: (Closed) htseq-count error on galaxy
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20 months ago by
costarc0
costarc0 wrote:

I modified my gff3 file to have a "gene_id" attribute but i keep having the error message: Fatal error: Unknown error occured Error occured when processing GFF file (line 4 of file /galaxy-repl/main/files/022/697/dataset_22697294.dat): Feature den1; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; pr

My gff3 file has the following attributes to exons:

NW_018657744.1 Gnomon exon 6016 6139 . - . "ad=den1; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 4956 5022 . - . "ad=den2; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 4746 4787 . - . "ad=den3; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 4567 4629 . - . "ad=den4; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 4123 4324 . - . "ad=den5; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 3535 3678 . - . "ad=den6; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 3182 3385 . - . "ad=den7; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1" NW_018657744.1 Gnomon exon 2387 2638 . - . "ad=den8; Parent=rna0; Dbxref=Geneden:110546218; gene_id= XM_021633030.1; gbkey=mRNA; gene=Serpinf2; product=serpin family F member 2%2C transcript variant X2 ; Gend=XM_021633030.1"

What can I do, please?

Thanks

ADD COMMENTlink written 20 months ago by costarc0

Hello costarc!

We believe that this post does not fit the main topic of this site.

Please ask https://biostar.usegalaxy.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 20 months ago by RamRS23k
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