AUGUSTUS Forum

Posted: **Fri Nov 20, 2015 12:57 pm**

Originally posted in the old forum by Han on 26.02.2013 - 06:28
Hi,
I'm working on a primate genome, previously I run augustus for gene prediction and it's works well. Now I want to use augustus to do gene prediction and include the cdna file. I've download human cdna file form ensemble.
Is this correct?

Code: Select all

>augustus --protein=on --introns=on --start=on --stop=on --cds=on --codingseq=on --gff3=on --cdna=cdna.fasta --outfile=NL_try_result --species=human NL_try.fasta

and I got this message:

Code: Select all

augustus: ERROR 
unknown parameter: "cdna"

Posted: **Fri Nov 20, 2015 12:57 pm**

by EJ Blom on 26.02.2013 - 09:14
I think you should convert the cdna entries to a hint file.
A nice tutorial is here:
http://bioinf.uni-greifswald.de/bioinf/ ... porateESTs

Posted: **Fri Nov 20, 2015 12:57 pm**

by Han on 26.02.2013 - 09:43
Thanks, I will try, hopefully it will work!

Posted: **Fri Nov 20, 2015 12:57 pm**

by Han on 28.02.2013 - 14:02
at the 3rd steps: Creates hints: I got this message: blat2hints.pl: command not found. any idea? I've copied the blat2hints.pl to my directory.

Posted: **Fri Nov 20, 2015 12:57 pm**

by katharina on 01.03.2013 - 15:22
Have you made it executable (e.g. using chmod)? Have you called it with its explicit path (if it was not added to your PATH variable), e.g. ./blat2hints.pl if it is located in the folder that you are currently working in?
Katharina

AUGUSTUS Forum

How to include cdna file

How to include cdna file

Re: How to include cdna file

Re: How to include cdna file

Re: How to include cdna file

Re: How to include cdna file