Closed RadPa closed 2 years ago
Hi Radhika,
It looks like the peaks were correctly annotated, but the attributes given in --show_attributes
were not properly shown (=NA) in the results. Can you share a few lines of your .agat.sort.gtf
? Then I can have a look why they are not found. Thanks!
Hi, Thank you for looking into it. This is the .gtf file, I have used.
NC_047627.1 Gnomon mRNA 16300 18139 . - . ID=XM_034259881.1;Parent=LOC117575606;db_xref=GeneID:117575606;gbkey=Gene;gene=LOC117575606;gene_biotype=protein_coding;gene_id=LOC117575606
NC_047627.1 Gnomon exon 16300 17237 . - . ID=exon-5;Parent=XM_034259881.1;db_xref=GeneID:117575606;exon_number=2;gbkey=mRNA;gene=LOC117575606;gene_id=LOC117575606;model_evidence=Supporting evidence includes similarity to: 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 5 samples with support for all annotated introns;product=uncharacterized LOC117575606%2C transcript variant X1;transcript_id=XM_034259881.1
NC_047627.1 Gnomon three_prime_UTR 16300 17216 . - . ID=nbis-three_prime_utr-17249;Parent=XM_034259881.1;db_xref=GeneID:117575606;exon_number=1;gbkey=mRNA;gene=LOC117575606;gene_id=LOC117575606;model_evidence=Supporting evidence includes similarity to: 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 5 samples with support for all annotated introns;product=uncharacterized LOC117575606%2C transcript variant X1;transcript_id=XM_034259881.1
NC_047627.1 Gnomon RNA 16300 18150 . - . ID=XR_004572888.1;Parent=LOC117575606;db_xref=GeneID:117575606;gbkey=Gene;gene=LOC117575606;gene_biotype=protein_coding;gene_id=LOC117575606
NC_047627.1 Gnomon exon 16300 17087 . - . ID=exon-3;Parent=XR_004572888.1;db_xref=GeneID:117575606;exon_number=3;gbkey=misc_RNA;gene=LOC117575606;gene_id=LOC117575606;model_evidence=Supporting evidence includes similarity to: 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 5 samples with support for all annotated introns;product=uncharacterized LOC117575606%2C transcript variant X2;transcript_id=XR_004572888.1
NC_047627.1 Gnomon exon 17156 17237 . - . ID=exon-2;Parent=XR_004572888.1;db_xref=GeneID:117575606;exon_number=2;gbkey=misc_RNA;gene=LOC117575606;gene_id=LOC117575606;model_evidence=Supporting evidence includes similarity to: 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 5 samples with support for all annotated introns;product=uncharacterized LOC117575606%2C transcript variant X2;transcript_id=XR_004572888.1
NC_047627.1 Gnomon CDS 17217 17237 . - 0 ID=cds-2;Parent=XM_034259881.1;db_xref=GeneID:117575606;exon_number=2;gbkey=CDS;gene=LOC117575606;gene_id=LOC117575606;product=uncharacterized protein LOC117575606;protein_id=XP_034115772.1;transcript_id=XM_034259881.1
NC_047627.1 Gnomon stop_codon 17217 17219 . - 0 ID=stop_codon-1;Parent=XM_034259881.1;db_xref=GeneID:117575606;exon_number=2;gbkey=CDS;gene=LOC117575606;gene_id=LOC117575606;product=uncharacterized protein LOC117575606;protein_id=XP_034115772.1;transcript_id=XM_034259881.1
NC_047627.1 Gnomon exon 17306 18139 . - . ID=exon-4;Parent=XM_034259881.1;db_xref=GeneID:117575606;exon_number=1;gbkey=mRNA;gene=LOC117575606;gene_id=LOC117575606;model_evidence=Supporting evidence includes similarity to: 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 5 samples with support for all annotated introns;product=uncharacterized LOC117575606%2C transcript variant X1;transcript_id=XM_034259881.1
Good Day Radhika
Hi Radhika,
Great, thanks for the file - I see the issue. The file you posted is in gff format (as supposed to gtf), which UROPA is unfortunately not able to read. There is a reference here on the difference between the different formats: https://m.ensembl.org/info/website/upload/gff.html. The main difference is in how the 'attribute' column is formatted, which differs between gff/gtf.
I just made a quick search and found this list of options for conversion from gff to gtf - I didn't try them myself, but maybe they are of help: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md
Hope this helps you out!
BR Mette
Thank you for the resources and Uropa. Both of them helped.
Good Day Radhika
Hi, I am unable to annotate the bed regions, even though I am not receiving any error messages. I am using RefSeq .gtf, enhanced by AGAT, and the gene_id is in LOC format. Uropa generated the output for all_hits and final_hits, but the regions were not annotated.
uropa -b merged.bed -g .agat.sort.gtf --show_attributes gene_id gene_name --feature_anchor start --distance 20000 10000 --feature gene
Can you please help? Thank you Radhika