Question: HTSeq error about gene_id
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gravatar for felipead66
12 months ago by
felipead6670
felipead6670 wrote:

gff-version 3

Pav_co3988703.1 augustus gene 1 195 0.7 - . ID=Pav_co3988703.1_g010.1.br;Note=PREDICTED: disease resistance protein RPM1-like Pav_co3988703.1 augustus exon 16 195 . - . ID=Pav_co3988703.1_g010.1.br:exon:1;

Parent=Pav_co3988703.1_g010.1.br
Pav_co3988703.1 augustus    CDS 16  195 0.7 -   0   ID=Pav_co3988703.1_g010.1.br:CDS:1;Parent=Pav_co3988703.1_g010.1.br
Pav_co3988737.1 maker   gene    29  998 .   -   .   ID=Pav_co3988737.1_g010.1.mk;Note=PREDICTED: peroxisomal 2,4-dienoyl-CoA reductase
Pav_co3988737.1 maker   exon    29  183 .   -   .   ID=Pav_co3988737.1_g010.1.mk:exon:3;Parent=Pav_co3988737.1_g010.1.mk
Pav_co3988737.1 maker   exon    517 739 .   -   .   ID=Pav_co3988737.1_g010.1.mk:exon:2;Parent=Pav_co3988737.1_g010.1.mk
Pav_co3988737.1 maker   exon    813 998 .   -   .   ID=Pav_co3988737.1_g010.1.mk:exon:1;Parent=Pav_co3988737.1_g010.1.mk
Pav_co3988737.1 maker   CDS 29  183 .   -   2   ID=Pav_co3988737.1_g010.1.mk:CDS:3;Parent=Pav_co3988737.1_g010.1.mk
Pav_co3988737.1 maker   CDS 517 739 .   -   0   ID=Pav_co3988737.1_g010.1.mk:CDS:2;Parent=Pav_co3988737.1_g010.1.mk

I try to use HTSeq to find counts for prunous avium but I get an error :

Error occured when processing GFF file (line 3 of file /home/maria/Documents/PAV_r1.0.genes.gff): Feature Pav_co3988703.1_g010.1.br:exon:1 does not contain a 'gene_id' attribute
[Exception type: ValueError, raised in count.py:79]

I have no idea what the gene_id could be replaced. Any help on that?

non-model gene_id htseq • 306 views
ADD COMMENTlink written 12 months ago by felipead6670
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