Set your variable variable and export them for your environment
THREADS=3
DATADIR=~/Share/GenomeAnnWorkshopDATA
SWISSPROTDB=$DATADIR/uniprot_sprot- These are the variables that needed to be exported to annotate the Arabidopsis taliana genome, I suggest to not change them.
SPECIES=Atal
BUSCODIR=$DATADIR
DIR=Tutorial.Arabidopsis
srSRAS='SRR5956435 SRR5956436'
longREADS='SRR23291376 SRR23291378'
LONGTYPE=pacbio
ASSEMBLY=$DATADIR/GCF_000001735.4_TAIR10.1_genomic.fna
TARGETCHR='NC_003070.9'
CHRNAME=chr1
CHR=$DATADIR/$SPECIES.$CHRNAME.fasta
ANNREF=$DATADIR/$SPECIES.$CHRNAME.gene.ncbi.gff
BRAKERGTF=$DATADIR/$SPECIES.braker_utr.$CHRNAME.gff3
STRAND='--rf'
LIBTYPE='first'
BUSCODB=embryophyta_odb12
MIKADOSCORE=$DATADIR/plants.yamlThese are the BUSCO profiles for the chromosome you're going to annotate:
| Results from dataset embryophyta_odb10: proteome |
|---|
| C:27.1%[S:14.4%,D:12.7%],F:0.3%,M:72.6%,n:1614 |
| 437 Complete BUSCOs (C) |
| 232 Complete and single-copy BUSCOs (S) |
| 205 Complete and duplicated BUSCOs (D) |
| 5 Fragmented BUSCOs (F) |
| 1172 Missing BUSCOs (M) |
| 1614 Total BUSCO groups searched |
And this is for the reference annotation:
| Results from dataset embryophyta_odb10: Chr1 |
|---|
| S:27.01%,D:0.19%,F:0.93%,I:0.00%,M:71.87%,n:1614 |
| 436 Complete and single-copy BUSCOs (S) |
| 3 Complete and duplicated BUSCOs (D) |
| 0 Incomplete (I) |
| 15 Fragmented BUSCOs (F) |
| 1160 Missing BUSCOs (M) |
| 1614 Total BUSCO groups searched |
You can use these stats as a comparison to evaluate the annotations you're going to generate.
- These are the variables that needed to be exported to annotate the Entomobrya proxima genome not to change.
SPECIES=Epro
BUSCODIR=$DATADIR
DIR=Tutorial.Springtail
srSRAS='SRR15910090'
longREADS='SRR15910089'
LONGTYPE=pacbio
ASSEMBLY=$DATADIR/GCA_029691765.1_ASM2969176v1_genomic.fna
TARGETCHR='CM056168.1'
CHRNAME=chr1
CHR=$DATADIR/$SPECIES.$CHRNAME.fasta
ANNREF=$DATADIR/$SPECIES.$CHRNAME.gene.maker.gff
BRAKERGTF=$DATADIR/$SPECIES.braker_utr.$CHRNAME.gff3
STRAND='--rf'
LIBTYPE='first'
BUSCODB=arthropoda_odb12
MIKADOSCORE=$DATADIR/insects.yaml| Results from dataset arthropoda_odb10: proteome |
|---|
| C:32.1%[S:28.9%,D:3.2%],F:1.9%,M:66.0%,n:1013 |
| 325 Complete BUSCOs (C) |
| 293 Complete and single-copy BUSCOs (S) |
| 32 Complete and duplicated BUSCOs (D) |
| 19 Fragmented BUSCOs (F) |
| 669 Missing BUSCOs (M) |
| 1013 Total BUSCO groups searched |
| Results from dataset arthropoda_odb10: Chr1 |
|---|
| S:30.40%,D:0.10%,F:1.09%,I:0.00%,M:68.41%,n:1013 |
| 308 Complete and single-copy BUSCOs (S) |
| 1 Complete and duplicated BUSCOs (D) |
| 0 Incomplete (I) |
| 11 Fragmented BUSCOs (F) |
| 693 Missing BUSCOs (M) |
| 1013 Total BUSCO groups searched |
- These are the variables that needed to be exported to annotate the Schistocerca gregaria genome not to change.
SPECIES=Sgre
BUSCODIR=$DATADIR
DIR=Tutorial.DesertLocust
srSRAS='SRR15423966 SRR15423964'
longREADS='SRR17978912'
LONGTYPE=pacbio
ASSEMBLY=$DATADIR/GCF_023897955.1_iqSchGreg1.2_genomic.fna
TARGETCHR='NC_064930.1'
CHRNAME=chr11
CHR=$DATADIR/$SPECIES.$CHRNAME.fasta
ANNREF=$DATADIR/$SPECIES.$CHRNAME.gene.ncbi.gff
BRAKERGTF=$DATADIR/$SPECIES.braker_utr.$CHRNAME.gff3
STRAND='--rf'
LIBTYPE='first'
BUSCODB=insecta_odb12
MIKADOSCORE=$DATADIR/insects.yaml| Results from dataset insecta_odb10: proteome |
|---|
| C:1.7%[S:1.0%,D:0.7%],F:0.2%,M:98.1%,n:1367 |
| 22 Complete BUSCOs (C) |
| 13 Complete and single-copy BUSCOs (S) |
| 9 Complete and duplicated BUSCOs (D) |
| 3 Fragmented BUSCOs (F) |
| 1342 Missing BUSCOs (M) |
| 1367 Total BUSCO groups searched |
| Results from dataset insecta_odb10: Chr11 |
|---|
| S:1.10%,D:0.00%,F:0.29%,I:0.00%,M:98.61%,n:1367 |
| 15 Complete and single-copy BUSCOs (S) |
| 0 Complete and duplicated BUSCOs (D) |
| 0 Incomplete (I) |
| 4 Fragmented BUSCOs (F) |
| 1348 Missing BUSCOs (M) |
| 1367 Total BUSCO groups searched |