M3 Lab4 - areed37/Andrew_Reed_EPP_531 GitHub Wiki

Last week results

#running busco for results
conda activate busco
busco -i braker_out/braker.aa -m protein -l fabales_odb10 -c 5 -o fabales_output

#Results from BRAKER
cat braker.gff3 | awk '{a[$3]++}END{for(k in a){print k,a[k]}}'
#mRNA 23929
#exon 130072
#CDS 130072
#intron 106143
#gene 21339
#start_codon 23924
#stop_codon 23925

Running EnTAP

#rename the amino acid sequence into something we can remember
mv braker.aa Ccanadensis_protein_hap1.fasta

#softlink that to a new folder
ln -s path_to/Ccanadensis_protein_hap1.fasta .

#load spack packages for entap
spack load diamond/ndn4ntw
spack load rsem
spack load interproscan
spack load transdecoder

/sphinx_local/software/EnTAP-1.0.0/bin/EnTAP \
--runP \
-i Ccanadensis_protein_hap1.fasta \
--ini /sphinx_local/software/EnTAP-1.0.0/entap_config_Oct2023.ini \
-d /sphinx_local/software/EnTAP-1.0.0/bin/uniprot_sprot.dmnd \
-t 5