GALBA commands

GALBA commands

Structural Analysis of GALBA Gene Prediction

Go to the directory for this activity

cd /home/{user}/train/Annotation_workshop/galba

Reformat the fasta file with the genome to an h5 format to be used by Helixer.

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 ~/.augustus

Use Mikado to generate metrics for each annotation.

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

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	118.00
Number of Transcripts	123.00
Transcripts per gene	1.04
Number of monoexonic genes	21.00
Monoexonic transcripts	21.00
Transcript mean size cDNA (bp)	1660.91
Transcript median size cDNA (bp)	1461.00
Min cDNA	396.00
Max cDNA	5494.00
Total exons	731.00
Exons per transcript	5.94
Exon mean size (bp)	279.47
CDS mean size (bp)	219.17
Transcript mean size CDS (bp)	1265.12
Transcript median size CDS (bp)	1029.00
Min CDS	129.00
Max CDS	5112.00
Intron mean size (bp)	163.89
5'UTR mean size (bp)	163.43
3'UTR mean size (bp)	232.36

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

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

Summarise both comparisions.

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

Visualise the the F1 metrics of all the comparisons.

less -s Mikado_compare/Athaliana_galba.f1.tsv