M3 Lab3 - areed37/Andrew_Reed_EPP_531 GitHub Wiki

Braker

#copy our masked genome and the star output
cp /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/Syri/Redbud_Genome_Hap2.fasta.masked .
cp /pickett_sphinx/projects/EPP531_AGA/lyadav_EPPAGA/Syri/Redbud_Hap1-rna_Aligned.sortedByCoord.out.bam .

wget https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11/Viridiplantae.fa.gz

#gunzip
gunzip Viridiplantae.fa.gz

#set path for braker and augustus files
export BRAKER_SIF=/sphinx_local/images/braker3_latest.sif
export AUGUSTUS_CONFIG_PATH=/home/areed37/miniconda3/envs/Busco_1/config
echo $AUGUSTUS_CONFIG_PATH


#running BRAKER
singularity exec -B $PWD /sphinx_local/images/braker3_latest.sif braker.pl --genome=Redbud_Genome_Hap2.fasta.masked \
--bam=Redbud_Hap1-rna_Aligned.sortedByCoord.out.bam \
--prot_seq=Viridiplantae.fa \
--workingdir=braker_hap1 \
--threads 5 \
--useexisting \
--gff3 \
--AUGUSTUS_CONFIG_PATH $AUGUSTUS_CONFIG_PATH \
--species=Ccanadensis

cat braker.gff3 | awk '{a[$3]++}END{for(k in a){print k,a[k]}}'

#give access and run busco on the protein fasta file (check lab 4 and check website for how to tweak for protein and not nucleotides)