How to include cdna file

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katharina
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How to include cdna file

Post by katharina »

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"
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katharina
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Re: How to include cdna file

Post by katharina »

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
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Re: How to include cdna file

Post by katharina »

by Han on 26.02.2013 - 09:43
Thanks, I will try, hopefully it will work!
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Re: How to include cdna file

Post by katharina »

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.
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Re: How to include cdna file

Post by katharina »

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?
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