GALBA commands

GALBA commands

Structural Analysis of GALBA Gene Prediction

Go to the directory for this activity.

cd /home/train/Annotation_workshop/galba

Run GALBA with a pre-trained model.

(
galba.pl \
    --skipAllTraining \
    --workingdir=output \
    --genome Inputs/Genome/Athaliana_447_TAIR10.Chr3-1065466-1464870.fa \
    --prot_seq=Inputs/Proteins/protein.fa \
    --gff3  \
    --verbosity=4 \
    --threads 2  \
    --species=arabidopsis  \
    --AUGUSTUS_CONFIG_PATH /opt/data/config
)

⚠️ Windows users:

galba.pl --skipAllTraining --workingdir=output --genome Inputs/Genome/Athaliana_447_TAIR10.Chr3-1065466-1464870.fa --prot_seq=Inputs/Proteins/protein.fa --gff3 --verbosity=4 --threads 2 --species=arabidopsis --AUGUSTUS_CONFIG_PATH /opt/data/config

Use Mikado to generate metrics for each annotation.

mkdir -p Mikado_stats; mikado util stats output/galba.gff3 Mikado_stats/galba.stats

Sumarise the statistics generated by Mikado.

parse_mikado_stats Mikado_stats/galba.stats > Mikado_stats/galba.stats.summary

Visualise the final output.

cat Mikado_stats/galba.stats.summary

Number of genes                   116.00
Number of Transcripts             121.00
Transcripts per gene              1.04
Number of monoexonic genes        20.00
Monoexonic transcripts            20.00
Transcript mean size cDNA (bp)    1676.10
Transcript median size cDNA (bp)  1462.00
Min cDNA                          396.00
Max cDNA                          5494.00
Total exons                       728.00
Exons per transcript              6.02
Exon mean size (bp)               278.58
CDS mean size (bp)                219.00
Transcript mean size CDS (bp)     1279.61
Transcript median size CDS (bp)   1038.00
Min CDS                           129.00
Max CDS                           5112.00
Intron mean size (bp)             163.79
5'UTR mean size (bp)              164.70
3'UTR mean size (bp)              231.79

Correct the gff positions to match the original chromosome positions.

bash  ./Scripts/offset_gff.sh output/galba.gff3 1065465  > galba_corrected.gff3

Use Mikado to compare the annotations to the reference annotation.

(
mikado compare \
    -r Inputs/Annotation/Athaliana_447_Araport11.Chr3-1065466-1464870.gene_exons.gff3 \
    -p galba_corrected.gff3  \
    -o Mikado_compare/galba
)

⚠️ Windows users:

mikado compare -r Inputs/Annotation/Athaliana_447_Araport11.Chr3-1065466-1464870.gene_exons.gff3 -p galba_corrected.gff3 -o Mikado_compare/galba

Do the same but only for CDS features.

(
mikado compare \
    -r Inputs/Annotation/Athaliana_447_Araport11.Chr3-1065466-1464870.gene_exons.gff3 \
    -p galba_corrected.gff3 \
    -eu  \
    -o Mikado_compare/galba_eu
)

⚠️ Windows users:

mikado compare -r Inputs/Annotation/Athaliana_447_Araport11.Chr3-1065466-1464870.gene_exons.gff3 -p galba_corrected.gff3 -eu -o Mikado_compare/galba_eu

Summarise both comparisons.

mikado util collect_compare -fmt tsv -l "all" -o Mikado_compare/Athaliana_galba Mikado_compare/*.stats

Visualise the F1 metrics of all the comparisons.

less -S Mikado_compare/Athaliana_galba.f1.tsv

Commands to clean up, i.e. return to only the original files.

cd /home/train/Annotation_workshop/galba
rm -rf -v !("Inputs"|"Scripts"|"commands.txt"|"Example_output")

⚠️ Windows users:

cd /home/train/Annotation_workshop/galba && rm -rf -v !("Inputs"|"Scripts"|"commands.txt"|"Example_output")