Braker

Discussions about BRAKER, the automated joint usage of GeneMark and AUGUSTUS.

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katharina
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Braker

Post by katharina »

Originally posted in the old forum by Rens Holmer on 05.03.2015 - 08:19
I recently started experimenting with using the Braker pipeline to incorporate RNA-seq into gene prediction. One of the problems I encounter is that while running braker in a certain folder, the files *.average_gene_length.out, *.f.bad.gtf and *.f.good.gtf are placed in the parent directory and can therefore not be found by braker.
Any ideas on what is causing this problem?
Also, is there no github (or equivalent) for braker/augustus?
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Re: Braker

Post by katharina »

by katharina on 06.03.2015 - 17:34
Can you please post the version numbers of BRAKER and GeneMark-ET that this question corresponds to?
Thank you.
Katharina
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Re: Braker

Post by katharina »

by Rens Holmer on 10.03.2015 - 09:06
braker.pl version 1.3
GeneMark-ES Suite version 4.21
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Re: Braker

Post by katharina »

by Rens Holmer on 11.03.2015 - 08:24
Dear Katharina,
Thank you for your response. In the meantime I have tracked the problem to a period (.) in the folder name. In the file filterGenemark.pl at line 156 the folder name is split on periods:
@_ = split(/\./, $genemark);
I have removed the periods from the folder name and that solved the problem. Perhaps this can be mentioned in the readme and be substituted for a more detailed regex in the future.
Cheers,
Rens
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Re: Braker

Post by katharina »

by katharina on 11.03.2015 - 17:19
Thank you. We will prepare a new release, probably, next week.
Best,
Katharina
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