Load arabidopsis annotation

[Bartusv]

I am trying to load the Arabidopsis annotation of https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes_transposons.gff

I have converted the file to GTF with AGAT and changed the feature names "Name" to "gene_name" and "Note" to "gene_type"

Resulting in a file structured like so:

##gtf-version 3 ChrM TAIR10 gene 273 734 . - . gene_id "ATMG00010"; ID "ATMG00010"; gene_name "ATMG00010"; gene_type "protein_coding_gene"; ChrM TAIR10 transcript 273 734 . - . gene_id "ATMG00010"; transcript_name "ATMG00010.1"; ID "ATMG00010.1"; level "1"; gene_name "ATMG00010.1"; Parent "ATMG00010"; original_biotype "mrna"; ChrM TAIR10 exon 273 734 . - . gene_id "ATMG00010"; transcript_name "ATMG00010.1"; ID "exon-215746"; Parent "ATMG00010.1"; ChrM TAIR10 CDS 273 734 . - 0 gene_id "ATMG00010"; transcript_name "ATMG00010.1"; ID "cds-197021"; Parent "ATMG00010.1"; ChrM TAIR10 gene 273 734 . - . gene_id "nbis-gene-35265"; ID "nbis-gene-35265"; ChrM TAIR10 transcript 273 734 . - . gene_id "nbis-gene-35265"; transcript_name "ATMG00010.1-Protein"; ID "ATMG00010.1-Protein"; Parent "nbis-gene-35265"; original_biotype "mrna"; ChrM TAIR10 exon 273 734 . - . gene_id "nbis-gene-35265"; transcript_name "ATMG00010.1-Protein"; ID "nbis-exon-197021"; Parent "ATMG00010.1-Protein"; ChrM TAIR10 CDS 273 734 . - 0 gene_id "nbis-gene-35265"; transcript_name "ATMG00010.1-Protein"; ID "cds-197021"; Parent "ATMG00010.1-Protein"; ChrM TAIR10 gene 8848 11415 . - . gene_id "ATMG00020"; ID "ATMG00020"; gene_name "ATMG00020"; gene_type "rRNA"; ChrM TAIR10 transcript 8848 11415 . - . gene_id "ATMG00020"; transcript_name "ATMG00020.1"; ID "ATMG00020.1"; level "1"; gene_name "ATMG00020.1"; Parent "ATMG00020"; original_biotype "rrna"; ChrM TAIR10 exon 8848 11415 . - . gene_id "ATMG00020"; transcript_name "ATMG00020.1"; ID "exon-215747"; Parent "ATMG00020.1"; ChrM TAIR10 gene 11918 12241 . + . gene_id "ATMG00030"; ID "ATMG00030"; gene_name "ATMG00030"; gene_type "protein_coding_gene"; ChrM TAIR10 transcript 11918 12241 . + . gene_id "ATMG00030"; transcript_name "ATMG00030.1"; ID "ATMG00030.1"; level "1"; gene_name "ATMG00030.1"; Parent "ATMG00030"; original_biotype "mrna"; ChrM TAIR10 exon 11918 12241 . + . gene_id "ATMG00030"; transcript_name "ATMG00030.1"; ID "exon-215748"; Parent "ATMG00030.1"; ChrM TAIR10 CDS 11918 12241 . + 0 gene_id "ATMG00030"; transcript_name "ATMG00030.1"; ID "cds-197022"; Parent "ATMG00030.1"; ChrM TAIR10 gene 11918 12241 . + . gene_id "nbis-gene-35266"; ID "nbis-gene-35266";

While plotting I encounter the following error though.

Error in geom_segment(): ! Problem while computing aesthetics. ℹ Error occurred in the 2nd layer. Caused by error: ! object 'group' not found Run rlang::last_trace() to see where the error occurred.

Could you please explain me what is going wrong?

[showteeth]

Hi,

The error message says object 'group' not found, I guess that this may be caused by grouping genes. Would you mind providing the modified GTF file, some test data and codes you used? These will help me find the error.

YB

[feiyu007]

I also meet this question. I modified my gtf file. finally, tish error occor. my gtf contents:

[m-jahn]

a reproducible example could help, a screenshot is not really usable

[m-jahn]

closed because of missing follow up information.