Hi there,
I'm currently conducting a transcriptomics study on Nicotiana benthamiana, and have reached a point where i would like to conduct a GO enrichment analysis using GOseq or topGO. Of course neither of these have N. benthamiana supported natively, so i would have to provide the GO mappings N. benthamiana genes myself. Other studies using the same sequence and annotations have used GOseq and topGO, but do not go into detail in their methods sections how they did this.
Of course i could simply feed a fasta of the DEGs into blast2go, but i don't actually have blast2go, and i feel like i'm missing something.
I cannot find a .GAF file (ontology annotation) in the annotations section of the N. benthamiana sequence website (ftp://ftp.solgenomics.net/genomes/Ni...tion/Niben101/). But i can see the GO terms for each gene in the .gff file, and they also provide a human readable functional annotations file (in .txt format) which contains GO terms (see picture at bottom). I could write a simple script to strip this .txt file down to a list of genes and GO terms, then use the method outlined here (https://bioinformatics.stackexchange...ation-file-gaf) to create a .GAF file, but i'm convinced there's an easier way.
Is there some way i can derive the GO mapping i need for GOseq from what is already provided?
I'm currently conducting a transcriptomics study on Nicotiana benthamiana, and have reached a point where i would like to conduct a GO enrichment analysis using GOseq or topGO. Of course neither of these have N. benthamiana supported natively, so i would have to provide the GO mappings N. benthamiana genes myself. Other studies using the same sequence and annotations have used GOseq and topGO, but do not go into detail in their methods sections how they did this.
Of course i could simply feed a fasta of the DEGs into blast2go, but i don't actually have blast2go, and i feel like i'm missing something.
I cannot find a .GAF file (ontology annotation) in the annotations section of the N. benthamiana sequence website (ftp://ftp.solgenomics.net/genomes/Ni...tion/Niben101/). But i can see the GO terms for each gene in the .gff file, and they also provide a human readable functional annotations file (in .txt format) which contains GO terms (see picture at bottom). I could write a simple script to strip this .txt file down to a list of genes and GO terms, then use the method outlined here (https://bioinformatics.stackexchange...ation-file-gaf) to create a .GAF file, but i'm convinced there's an easier way.
Is there some way i can derive the GO mapping i need for GOseq from what is already provided?
