View Single Post
Old 06-05-2012, 07:33 PM   #1
Daniel Fernandez
Member
 
Location: Lima. Perú

Join Date: Nov 2011
Posts: 31
Default Exonerate GFF in Artemis

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:

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

Last edited by Daniel Fernandez; 06-06-2012 at 11:00 AM.
Daniel Fernandez is offline   Reply With Quote