Question: Get summary of augustus ouput (gff)
0
gravatar for Chvatil
2.4 years ago by
Chvatil50
Chvatil50 wrote:

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 :)

gff augustus • 1.1k views
ADD COMMENTlink modified 2.4 years ago by goodez480 • written 2.4 years ago by Chvatil50
1

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Mehmet600
1
gravatar for goodez
2.4 years ago by
goodez480
United States
goodez480 wrote:

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.

ADD COMMENTlink written 2.4 years ago by goodez480

OK I'll try this thank you :)

ADD REPLYlink written 2.4 years ago by Chvatil50
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