Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.

Question

[Vijith]

I am seeking help with Augustus gene prediction! I am performing a whole genome assembly of a plant species. I have completed the gene prediction using the Augustus pipeline. The output file is of format .gff . Now I want to perform the gene annotation by performing BLAST for which I need the coding sequences in a .fasta. file.

This is the method that I've thought of approaching.

1. Use the perl script getAnnoFasta.pl to get the amino acid sequence, and later the sequence in fasta format.

But I've also seen others mention various other tools at gff3 to CDS fasta. Can someone provide some insights, as to what tool could be of assistance.

[Juke34]

You can get a look here Extracting genomic feature sequences from GTF/GFF files with AGAT

[Vijith]

I have tried installing AGAT. But it failed the tests. for example. ~

/AGAT$ perl Makefile.PL
Warning: prerequisite Bio::DB::Fasta 0 not found.
Warning: prerequisite Bio::DB::Taxonomy 0 not found.
Warning: prerequisite Bio::Ontology::OntologyEngineI 0 not found.
Warning: prerequisite Bio::OntologyIO::obo 0 not found.
Warning: prerequisite Bio::Seq 0 not found.
Warning: prerequisite Bio::SeqIO 0 not found.
Warning: prerequisite Bio::Tools::CodonTable 0 not found.
Warning: prerequisite Bio::Tools::GFF 0 not found.
Warning: prerequisite File::Share 0 not found.
Warning: prerequisite LWP::Protocol::https 0 not found.
Warning: prerequisite LWP::UserAgent 0 not found.
Warning: prerequisite List::MoreUtils 0 not found.
Warning: prerequisite Moose 0 not found.
Warning: prerequisite Sort::Naturally 0 not found.
Warning: prerequisite Term::ProgressBar 0 not found.
Warning: prerequisite YAML 0 not found.
Generating a Unix-style Makefile
Writing Makefile for AGAT
Writing MYMETA.yml and MYMETA.json                                                                                                                                                                                                                                                                                                                                                By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process. The `perl` version is `v5.38.2`, and I was installing it manually following `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 libfile-sharedir-install-perl libyaml-perl liblwp-protocol-https-perl libterm-progressbar-perl`

[Vijith]

By doing some online search, I tried installing one module cpan Bio::DB::Fasta and it is running like a never-ending installation process. The perl version is v5.38.2, and I was installing it manually following 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 libfile-sharedir-install-perl libyaml-perl liblwp-protocol-https-perl libterm-progressbar-perl

[Juke34]

Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgrade your perl version.