Hi,
May be this is very simple question, I'm beginner in bioinformatics.
I'm trying to run exonerate, I tested with a partial chr1 of A. thaliana, and extract its mRNA, only for test. I generate its GFF of the query, the partial chr1, and the GFF of its genes, but when I tried to load in artemis, it doesn't work, when I load the GFF, query or target, only show the partial chr1 fasta.
It is not a problem with artemis, because I load the augustus ab-inito.GFF and work.
These are my commands:
May be this is very simple question, I'm beginner in bioinformatics.
I'm trying to run exonerate, I tested with a partial chr1 of A. thaliana, and extract its mRNA, only for test. I generate its GFF of the query, the partial chr1, and the GFF of its genes, but when I tried to load in artemis, it doesn't work, when I load the GFF, query or target, only show the partial chr1 fasta.
It is not a problem with artemis, because I load the augustus ab-inito.GFF and work.
These are my commands:
Code:
exonerate -q At.chr1.fa -Q dna -t At.genes.fa -T dna -m e2g --refine region --showalignment no --showvulgar no --showquerygff yes > At.chr1.gff exonerate -q At.chr1.fa -Q dna -t At.genes.fa -T dna -m e2g --refine region --showalignment no --showvulgar no --showtargetgff yes > At.genes.gff artemis At.chr1.fa + At.chr1.gff # only show At.chr1.fa artemis At.chr1.fa + At.genes.gff # only show At.chr1.fa artemis At.chr1.fa + At.chr1.gff + At.genes.gff # only show At.chr1.fa