gff3ToGenePred

Question

[bestone]

Hello guys, I downloaded gff3ToGenePred and tried to convert the gff3 file in Apricot, but gff3ToGenePred gave an error even though it was loaded. this is the code I am using

gff3ToGenePred -genePredExt /Users/uguremre/snpEff/snpEff/stella.gff3 AT_refGene.txt

[Juke34]

What type of error?

[bestone]

this is the error. : zsh: command not found: gff3ToGenePred I am not sure where I went wrong

[Juke34]

The error is not related to the tool. It is you terminal ( I guess you are using a Mac) that tell you that the tool is not available. You are not in the proper directory, or provide the path to the tool

[bestone]

thank you for your reply. Yes, I am using a Mac. Annovar is in a separate file, but I didn't open a new file for gff3ToGenePred. Annovar and gff3ToGenePred are in separate places. they will be in the same file?