How to read the AUGUSTUS results

Question

[Shin Taguchi]

Hi, everyone.

I used AUGUSTUS to make a genetic prediction for a certain fish, but I don't know how to read the results. I mainly do not understand the following three points.

1.What does "sequence number" mean? How is it different from scaffold number?

2.What does "none" mean? Does it mean that the gene could not be predicted?

# This output was generated with AUGUSTUS (version 3.4.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initializing the parameters using config directory /usr/local/config/ ...
# zebrafish version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(0.999), CTG(0.000667), TTG(0)
# Looks like 201123_Psic.polished.scaffold.masked.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 1306, name = scaffold_0) -----
#
# Predicted genes for sequence number 1 on both strands
# (none)

3.The end of the output file looked like this. It appears to end in the middle of the file, is this a correct genetic prediction?

# ----- prediction on sequence number 24 (length = 103991, name = scaffold_39) -----
#
# Predicted genes for sequence number 24 on both strands

If anyone knows, please let me know.

Answer 1

[Istvan Albert]

Visualize your data in IGV, load your custom genome and your annotations.

Also, generate statistics on coverage over the features, etc.

That way, you can gain a better understanding of the results rather than trying to decipher tracing messages produced by the tool.

I would not put too much stock into the "correct" interpretation of the random progress messages. Those are not the scientific output and are there just to remind the user of the tool's progress.

[Shin Taguchi]

Istvan Albert

Thank you for your comment! I will try to visualize the results using IGV.