Another Gtf/Gff Analysis Toolkit
Suite of tools to handle gene annotations in any GTF/GFF format.
Documentation >>here<<
Previous documentation until v1.4.0 (readthedocs) here
AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format. Over the years it has been enriched by many many tools to perform just about any tasks that is possible related to GTF/GFF format files (sanitizing, conversions, merging, modifying, filtering, FASTA sequence extraction, adding information, etc). Comparing to other methods AGAT is robust to even the most despicable GTF/GFF files.
Standardize/sanitize any GTF/GFF file into a comprehensive GFF3 format (script with _sp_
prefix)
agat_convert_sp_gxf2gxf.pl
|Convert many formats
agat_convert_sp_gff2bed.pl
|agat_convert_sp_gff2gtf.pl
|agat_sp_gff2tsv.pl
|agat_convert_sp_minimap2_bam2gff.pl
|agat_sp_gff2zff.pl
|agat_convert_sp_gxf2gxf.pl
|agat_convert_bed2gff.pl
|agat_convert_embl2gff.pl
|agat_convert_genscan2gff.pl
|agat_convert_mfannot2gff.pl
|Perform numerous tasks (Just about anything that is possible)
agat_sp_statistics.pl
|agat_sp_functional_statistics.pl
|agat_sp_extract_sequences.pl
|agat_sp_extract_attributes.pl
|agat_sp_complement_annotations.pl
|agat_sp_merge_annotations.pl
|agat_sp_filter_by_ORF_size.pl
|agat_sp_keep_longest_isoform.pl
|agat_sp_add_introns.pl
|agat_sp_fix_cds_phases.pl
|agat_sp_manage_IDs.pl
|agat_sp_manage_UTRs.pl
|agat_sp_manage_introns.pl
|agat_sp_manage_functional_annotation.pl
|agat_sp_sensitivity_specificity.pl
|agat_sp_compare_two_annotations.pl
|agat_sp_compare_two_BUSCOs.pl
|About the GTF/GFF fromat
The GTF/GFF formats are 9-column text formats used to describe and represent genomic features.
The formats have quite evolved since 1997, and despite well-defined specifications existing nowadays they have a great flexibility allowing holding wide variety of information.
This flexibility has a drawback aspect, there is an incredible amount of flavour of the formats, that can result in problems when using downstream programs.
For a complete overview of the GTF/GFF formats have a look here.
# get the chosen AGAT container version
docker pull quay.io/biocontainers/agat:1.4.2--pl5321hdfd78af_0
# use an AGAT's tool e.g. agat_convert_sp_gxf2gxf.pl
docker run quay.io/biocontainers/agat:1.4.2--pl5321hdfd78af_0 agat_convert_sp_gxf2gxf.pl --help
# get the chosen AGAT container version
singularity pull docker://quay.io/biocontainers/agat:1.4.2--pl5321hdfd78af_0
# run the container
singularity run agat_1.4.2--pl5321hdfd78af_0.sif
agat_convert_sp_gxf2gxf.pl --help
conda install -c bioconda agat
conda update agat
conda uninstall agat
conda install r-base
), through CRAN (See here for a nice tutorial) or using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions). R is optional and can be used to perform some plots. You will need to install the perl depency Statistics::R
Perl >= 5.8cpanm install bioperl Clone Graph::Directed LWP::UserAgent Carp Sort::Naturally File::Share File::ShareDir::Install Moose YAML LWP::Protocol::https Term::ProgressBar
conda env create -f conda_environment_AGAT.yml
conda activate agat
conda install perl-bioperl perl-clone perl-graph perl-lwp-simple perl-carp perl-sort-naturally perl-file-share perl-file-sharedir-install perl-moose perl-yaml perl-lwp-protocol-https perl-term-progressbar
using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions)apt install libbio-perl-perl libclone-perl libgraph-perl liblwp-useragent-determined-perl libstatistics-r-perl libcarp-clan-perl libsort-naturally-perl libfile-share-perl libfile-sharedir-perl libfile-sharedir-install-perl libyaml-perl liblwp-protocol-https-perl libterm-progressbar-perl
conda install r-base
), through CRAN (See here for a nice tutorial) or using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions).conda install perl-statistics-r
), using cpan/cpanm (cpanm install Statistics::R
), or your package management tool (apt install libstatistics-r-perl
)<sup>*</sup>If dependencies are missing you will be warn. Please refer to the [Install prerequisites](#install-prerequisites) section.
**Remark**: On MS Windows, instead of make you'd probably have to use dmake or nmake depending the toolchain you have.
#### Update AGAT
From the folder where the repository is located.
git pull # Update the code
git checkout v0.1 # use version v0.1 (See releases tab for a list of available versions)
perl Makefile.PL # Check all the dependencies*
make # Compile
make test # Test
make install # Install
perl uninstall_AGAT
script_name.pl -h
As AGAT is a toolkit, it contains a lot of tools. The main one is agat_convert_sp_gxf2gxf.pl
that allows to check, fix, pad missing information (features/attributes) of any kind of gtf and gff to create complete, sorted and standardised gff3 format.
All the installed scripts have the agat_
prefix.
To have a look to the available tools you have several approaches:
agat --tools
agat_
in your terminal followed by the The gff file will be charged in memory in a specific data structure facilitating the access to desired features at any time.
It has a memory cost but make life smoother. Indeed, it allows to perform complicated tasks in a more time efficient way.
Moreover, it allows to fix all potential errors in the limit of the possibilities given by the format itself.
See the AGAT parser section for more information about it.
The gff file is read and processed from its top to the end line by line without sanity check (e.g. relationship between the features). This is memory efficient.
All tools with agat_sp_
prefix will parse and slurps the entire data into a specific data structure.
Below you will find more information about peculiarity of the data structure,
and the parsing approach used.
$omniscient{other}{header} = header information from the beginning of the file starting by #
$omniscient{level1}{tag_l1}{level1_id} = feature <= tag could be gene, match
$omniscient{level2}{tag_l2}{idY} = @featureListL2 <= tag could be mRNA,rRNA,tRNA,etc. idY is a level1_id (know as Parent attribute within the level2 feature). The @featureListL2 is a list to be able to manage isoform cases.
$omniscient{level3}{tag_l3}{idZ} = @featureListL3 <= tag could be exon,cds,utr3,utr5,etc. idZ is the ID of a level2 feature (know as Parent attribute within the level3 feature). The @featureListL3 is a list to be able to put all the feature of a same tag together.
agat_config.yml
information in that structure:$omniscient{config}{parameter1} = value parameter1
$omniscient{config}{parameter2} = value parameter2
feature_levels.yaml
information in that structure:$omniscient{other}{level}{level1}{featureTypeX} = value featureTypeX (standalone, topfeature)
$omniscient{other}{level}{level2}{featureTypeY} = value featureTypeY
$omniscient{other}{level}{level2}{featureTypeZ} = value featureTypeZ
The AGAT parser phylosophy:
/!\ Cases with only level3 features (i.e rast or some prokka files), sequential parsing may not work as expected if Parent/ID gene_id/transcript_id attributes are missing. Indeed all features will be the child of only one newly created Parent. To create a parent per feature or group of features, a common tag must be used to group them correctly (by default gene_id
and locus_tag
but you can set up the ones of your choice)
To resume by priority of way to parse: Parent/child relationship > locus_tag > sequential.
The parser may used only one or a mix of these approaches according of the peculiarity of the gtf/gff file you provide.
AGAT was tested on 42 different types of GTF/GFF of different flavours or/and containing errors.
Below few are listed but you can find the full list of them into the t/gff_syntax
directory.
##gff-version 3
Tob1_contig1 Prodigal:2.60 CDS 476 670 . - 0 ID=Tob1_00001;locus_tag=Tob1_00001;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 CDS 34266 35222 . + 0 ID=Tob1_00024;locus_tag=Tob1_00024;product=hypothetical protein
Tob1_contig1 SignalP:4.1 sig_peptide 34266 34298 . + 0 inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 33;product=putative signal peptide
Tob1_contig1 Prodigal:2.60 CDS 35267 37444 . - 0 ID=Tob1_00025;locus_tag=Tob1_00025;
Tob1_contig1 SignalP:4.1 sig_peptide 37420 37444 . - 0 inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 25;product=putative signal peptide
Tob1_contig1 Prodigal:2.60 CDS 38304 39338 . - 0 ID=Tob1_00026;locus_tag=Tob1_00026;
agat_convert_sp_gxf2gxf.pl --gff 8_test.gff
##gff-version 3
Tob1_contig1 Prodigal:2.60 gene 476 670 . - 0 ID=nbis_NEW-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 mRNA 476 670 . - 0 ID=nbis_nol2id-cds-1;Parent=nbis_NEW-gene-1;locus_tag=Tob1_00001;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 exon 476 670 . - . ID=nbis_NEW-exon-1;Parent=nbis_nol2id-cds-1;locus_tag=Tob1_00001;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 CDS 476 670 . - 0 ID=Tob1_00001;Parent=nbis_nol2id-cds-1;locus_tag=Tob1_00001;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 gene 34266 35222 . + 0 ID=nbis_NEW-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 mRNA 34266 35222 . + 0 ID=nbis_nol2id-cds-2;Parent=nbis_NEW-gene-2;locus_tag=Tob1_00024;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 exon 34266 35222 . + . ID=nbis_NEW-exon-2;Parent=nbis_nol2id-cds-2;locus_tag=Tob1_00024;product=hypothetical protein
Tob1_contig1 Prodigal:2.60 CDS 34266 35222 . + 0 ID=Tob1_00024;Parent=nbis_nol2id-cds-2;locus_tag=Tob1_00024;product=hypothetical protein
Tob1_contig1 SignalP:4.1 sig_peptide 34266 34298 . + 0 ID=sig_peptide-1;Parent=nbis_nol2id-cds-2;inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 33;product=putative signal peptide
Tob1_contig1 Prodigal:2.60 gene 35267 37444 . - 0 ID=nbis_NEW-gene-3;locus_tag=Tob1_00025
Tob1_contig1 Prodigal:2.60 mRNA 35267 37444 . - 0 ID=nbis_nol2id-cds-3;Parent=nbis_NEW-gene-3;locus_tag=Tob1_00025
Tob1_contig1 Prodigal:2.60 exon 35267 37444 . - . ID=nbis_NEW-exon-3;Parent=nbis_nol2id-cds-3;locus_tag=Tob1_00025
Tob1_contig1 Prodigal:2.60 CDS 35267 37444 . - 0 ID=Tob1_00025;Parent=nbis_nol2id-cds-3;locus_tag=Tob1_00025
Tob1_contig1 SignalP:4.1 sig_peptide 37420 37444 . - 0 ID=sig_peptide-2;Parent=nbis_nol2id-cds-3;inference=ab initio prediction:SignalP:4.1;note=predicted cleavage at residue 25;product=putative signal peptide
Tob1_contig1 Prodigal:2.60 gene 38304 39338 . - 0 ID=nbis_NEW-gene-4;locus_tag=Tob1_00026
Tob1_contig1 Prodigal:2.60 mRNA 38304 39338 . - 0 ID=nbis_nol2id-cds-4;Parent=nbis_NEW-gene-4;locus_tag=Tob1_00026
Tob1_contig1 Prodigal:2.60 exon 38304 39338 . - . ID=nbis_NEW-exon-4;Parent=nbis_nol2id-cds-4;locus_tag=Tob1_00026
Tob1_contig1 Prodigal:2.60 CDS 38304 39338 . - 0 ID=Tob1_00026;Parent=nbis_nol2id-cds-4;locus_tag=Tob1_00026
##gff-version 3
#!gff-spec-version 1.14
#!source-version NCBI C++ formatter 0.2
##Type DNA NC_003070.9
NC_003070.9 RefSeq source 1 30427671 . + . organism=Arabidopsis thaliana;mol_type=genomic DNA;db_xref=taxon:3702;chromosome=1;ecotype=Columbia
NC_003070.9 RefSeq gene 3631 5899 . + . ID=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 3631 3913 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 3996 4276 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 4486 4605 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 4706 5095 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 5174 5326 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq exon 5439 5899 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 3760 3913 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 3996 4276 . + 2 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 4486 4605 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 4706 5095 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 5174 5326 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq CDS 5439 5627 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq start_codon 3760 3762 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
NC_003070.9 RefSeq stop_codon 5628 5630 . + 0 ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
agat_convert_sp_gxf2gxf.pl --gff 8_test.gff
##gff-version 3
#!gff-spec-version 1.14
#!source-version NCBI C++ formatter 0.2
##Type DNA NC_003070.9
NC_003070.9 RefSeq source 1 30427671 . + . ID=source-1;chromosome=1;db_xref=taxon:3702;ecotype=Columbia;mol_type=genomic DNA;organism=Arabidopsis thaliana
NC_003070.9 RefSeq gene 3631 5899 . + . ID=nbis_NEW-gene-1;locus_tag=AT1G01010
NC_003070.9 RefSeq mRNA 3631 5899 . + . ID=NC_003070.9:NAC001;Parent=nbis_NEW-gene-1;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 3631 3913 . + . ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 3996 4276 . + . ID=nbis_NEW-exon-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 4486 4605 . + . ID=nbis_NEW-exon-2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 4706 5095 . + . ID=nbis_NEW-exon-3;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 5174 5326 . + . ID=nbis_NEW-exon-4;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq exon 5439 5899 . + . ID=nbis_NEW-exon-5;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 3760 3913 . + 0 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 3996 4276 . + 2 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 4486 4605 . + 0 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 4706 5095 . + 0 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 5174 5326 . + 0 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq CDS 5439 5627 . + 0 ID=nbis_NEW-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq five_prime_UTR 3631 3759 . + . ID=nbis_NEW-five_prime_utr-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
NC_003070.9 RefSeq start_codon 3760 3762 . + 0 ID=nbis_NEW-start_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq stop_codon 5628 5630 . + 0 ID=nbis_NEW-stop_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
NC_003070.9 RefSeq three_prime_UTR 5628 5899 . + . ID=nbis_NEW-three_prime_utr-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
##gff-version 3
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
agat_convert_sp_gxf2gxf.pl --gff 18_test.gff
##gff-version 3
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
scaffold789 maker gene 558184 564780 . + . ID=CLUHARG00000003852;Name=PF11_0240
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006146;Parent=CLUHARG00000003852
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
scaffold789 maker exon 564171 564235 . + . ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker CDS 564171 564235 . + 0 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
scaffold789 maker mRNA 558184 564780 . + . ID=CLUHART00000006147;Parent=CLUHARG00000003852
scaffold789 maker exon 558184 560123 . + . ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
scaffold789 maker exon 561401 561519 . + . ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
scaffold789 maker exon 562057 562121 . + . ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
scaffold789 maker exon 564372 564780 . + . ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
scaffold789 maker CDS 558191 560123 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 561401 561519 . + 2 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 562057 562121 . + 0 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker CDS 564372 564588 . + 1 ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
scaffold789 maker five_prime_UTR 558184 558190 . + . ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
scaffold789 maker three_prime_UTR 564589 564780 . + . ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
This work has not been published (I will think about it) but you can cite it as follow:
Dainat J. 2022. Another Gtf/Gff Analysis Toolkit (AGAT): Resolve interoperability issues and accomplish more with your annotations. Plant and Animal Genome XXIX Conference. https://github.com/NBISweden/AGAT.
or/and (Adapt the AGAT version to the one you used):
Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format.
(Version v1.4.1). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
See here for examples of publications using AGAT.
See Troubleshooting section form the doc here.