Entering edit mode
16 months ago
bestone
▴
30
Hello guys, I am trying to run annovar using this code:
annovar/table_annovar.pl annovar/output.avinput \
annovar/AT_refGeneMrna.fasta \
annovar/AT_refGeneMrna.txt \
-out myanno \
-remove \
-protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all \
-operation g,r,r,f,f,f,f \
-nastring .
But I am getting the error mentioned in the title (Error: the required database file annovar/AT_refGeneMrna.txt/hg18_refGene.txt does not exist
). Could you please help me with this issue? I created the avinput file and mrna.fasta files using annovar. I am using apricot file I am not working with human
Are you sure annovar databases exist for apricot?
Side note: I've cleaned up your post a little bit so people don't have to put things together in their head to see the command and error. Just because you mentioned the error in the title does not mean you shouldn't mention it in the body of the post as well.
Thank you for the necessary arrangements and cleaning, yes, we can do it for the apricot genome, unlike humans, but I could not pass this step.
I don't understand - if you're using apricot genome, why are your annotation databases human (1000genome, ESP)?