Get summary of augustus ouput (gff)

Question

[Chvatil]

Hi all, I made 4 augustus run for all my genomes assembly and get 4 gff files.

Does someone know a programme which plot the results in sumarry, or only creat a summary table with number of gene predicted, number of complet ones (start + stop) etc? ? Thank you :)

[Mehmet]

Additionally, you can use getAnnoFasta.pl scprit in script directory of Augustus to get amino acid sequences of predicted genes.Assume you get aminoacidsequences.aa as an output. Later, you can use stats aminoacidsequences.aa

Answer 1

[goodez]

A good place to start would be some simple command line tricks. You won't need to install anything just open up a unix terminal.

To see how many gene features are in your gff:

awk '$3=="gene"' your_file.gff | wc -l

This gives you the total number of gene features. You can play around with this command to view other features like "transcript". Also you can look at $4 and $5 columns which are the start and end of each feature.

[Chvatil]

OK I'll try this thank you :)