To resume:
Download gtf files of the investigated genome
To get a subset of this data (only one chromosome as example) do
awk '{if ($1 == "Chromosome") print $0 }' file.gtf >> file_chromosome.gtf
Download genome *fasta *of the investigated genome
Use the script gff2gbSmallDNA from augustus package
gff2gbSmallDNA.pl gff-file seq-file max-size-of-gene-flanking-DNA output-file
Get a random gene set from the file obtained previously with the script randomSplit from augustus package
randomSplit.pl geneSet.gb nbGene
(You should get 2 files. One gene set for training, the other to test the model obtained by the training)
Preparation of augustus directories and files (drosophila species as example)
new_species.pl --species=drosophila
Training augustus
etraining --species=species genesSet.gb.train
Launch Augustus:
augustus --gff3=on --species=drosophila genesSet.gb.test | tee drosophila_test.out
Look Results
grep -A 22 Evaluation drosophila_test.out
Hi! I am trying to train augustus for glycine and I am following the steps you have mentioned.
While using gff2gbSmallDNA.pl . I am getting error Couldn't open gff.
While using autoAug.pl following error:
Error: The environment variable AUGUSTUS_CONFIG_PATH is not define
Can you please help me with this
Hi,
Look at these webpages, they contain everything you have to know.
Hi,
when I run gff2gbSmallDNA.pl, it finishes without any error and doesn't give any output.
gff-file : I have list of intron coordinates gff
example :
contig100067 b2h intron 730 761 0 . . grp=TRINITY_DN11987_c1_g42_i1;pri=4;src=E
contig100067 b2h intron 1773 1807 0 . . grp=TRINITY_DN11987_c1_g42_i1;pri=4;src=E
seq-file: list of contig in fasta
I don't know how to go about it. could you please help with the same ?
My Regards,
Prasoon
Hi,
Can you please write what command you have used? and Did you check seq names in fasta file? The seq names should be same in the gff file? what option did you use in your command?
/scripts/gff2gbSmallDNA.pl gff-file seq-file max-size-of-gene-flanking-DNA output-file [options]
here is my command:
/scripts/gff2gbSmallDNA.pl 1.gff 1.fasta 100 1.small.gb
and files used in the command: head 1.gff
1 artemis gene 6521 7714 . - . ID=1.1
1 artemis mRNA 6521 7714 . - . ID=1.1t;Parent=1.1
1 artemis exon 6521 6634 . - . ID=1.1.1;Parent=1.1t
1 artemis CDS 6521 6634 . - . ID=cds.1.1.1;Parent=1.1t
1 artemis exon 6711 6939 . - . ID=1.1.2;Parent=1.1t
1 artemis CDS 6711 6939 . - . ID=cds.1.1.2;Parent=1.1t
1 artemis exon 6982 7130 . - . ID=1.1.3;Parent=1.1t
1 artemis CDS 6982 7130 . - . ID=cds.1.1.3;Parent=1.1t
1 artemis exon 7215 7353 . - . ID=1.1.4;Parent=1.1t
1 artemis CDS 7215 7353 . - . ID=cds.1.1.4;Parent=1.1t
head 1.fa
>1 all_bases
tccttactggatcatgaaaaatcaatggggggaagaatggggagagagcggattctttag
agctatccgcggcactaacaacatgctggttggggactggaactaccaagttcaacttta
aaattttcttaaatctttattatgatacaattttatggataaagcgctaaatttctattg
actttggatcatctgttgaggcagaaatgttgtgtgtttaaaactgtcttgtatttaact
aaataaatctactgaaacttttt
tgtagctccggtgaaaccagctgcttttaggctgtag
ggagaacgataaaaaattttgtctctgcagcgacaaaaagtggaaatcgcataaaacaca
aacattgccacgacggaaaaaaagacgttgtatgactgtttaataaacaaaactatttaa
ttttctagtttcgtcaaattccaaattgtcgctcatcttccgacagctatcttcattaaa
attcaaaaattttacttgcgaattgaggaaatcccgtttcttatcttcccgaagagaaag
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