Gff not recognized

[m-bogaerts]

Hello!

I have some issues using the read_gff3 function. I am getting a gff from exonerate and I get the following error:
Harmonizing attribute names
• ID -> feat_id
• Parent -> parent_ids
• Align -> align
• Query -> query
Error in bind_rows():
! Can't combine ..1$feat_id and ..2$feat_id .
Run rlang::last_trace() to see where the error occurred.
Warning message:
This looks like a gff2/gtf file. This is usually fine, but given the ambigious definition of this format, it is not guaranteed that gene models are always captured correctly. exons/CDS might not be recognized as belonging to the same gene, etc. Also note: types and attributes are as far as possible converted to match gff3 standards (transcript -> mRNA, 5'/3'UTR -> five/three_prime_UTR, ...)

I tried to convert my gff into gtf using AGAT but I have the same problem. The format of my gff/gtf is the following one:
##gtf-version X

GFF-like GTF i.e. not checked against any GTF specification. Conversion based on GFF input, standardised by AGAT.

##source-version exonerate:protein2genome:local 2.4.0
BnS exonerate:protein2genome:local gene 214068 243275 1956 + . gene_id "1"; ID "agat-gene-8"; gene_orientation "+"; identity "100.00"; sequence "URC25299.1"; similarity "100.00";
BnS AGAT mRNA 214068 243275 . + . gene_id "1"; transcript_id "agat-rna-10"; ID "agat-rna-10"; Parent "agat-gene-8";

Is there something I am doing wrong?

Thank you in advance!

[thackl]

Could you attach your gtf/gff as a file (paperclip icon in the toolbar above the text box)? Thanks!

[m-bogaerts]

Thank very much for your answer. Please, find attached the gtf file.

dtol_habn_hab4_hab2_alpha_protein.gtf.txt

[thackl]

Try it now. And let me know if there are still problems

[m-bogaerts]

Thank you very much, it now works and recognize all the annotation types:
Harmonizing attribute names
• ID -> feat_id
• Parent -> parent_ids
• Align -> align
• Query -> query
Features read

A tibble: 8 × 3

source type n

1 AGAT mRNA 27
2 exonerate:protein2genome:local CDS 27
3 exonerate:protein2genome:local exon 27
4 exonerate:protein2genome:local gene 11
5 exonerate:protein2genome:local intron 16
6 exonerate:protein2genome:local similarity 11
7 exonerate:protein2genome:local splice3 16
8 exonerate:protein2genome:local splice5 16

However, when plotting them, it only plots few mRNA and CDS (see picture attached). Since I am interested in plotting exons particularly, is something I can do for that?

Thank you very much in advance.

[thackl]

Something like this?

# show everything first
g0 <- read_feats("issue_177/dtol_habn_hab4_hab2_alpha_protein.gtf")

gggenomes(g0) +
  geom_gene() +  # geom_gene specifically parses mRNA, CDS and introns from gene track
  geom_seq() +
  geom_feat(aes(color=type), data=feats(genes)) # geom_feat generically plots any feature from any track

# focus on features of interest
gggenomes(g0) |> 
  focus() + # zoom in on regions with actual feature (ignore intergeneic space)
  geom_gene() +
  geom_seq() +
  geom_feat(aes(color=type), 
            data=feats(genes, type %in% c("exon", "intron")), # filter of features of interest
            position = position_nudge(y=.2)) # move them up in the plot

[m-bogaerts]

That's exactly what I was looking for. Thank you very much for your answer!