Using the Trandsdecoder and the Trinity assembly, a deduced proteome was generated.

In Jupyter…

1. extract the long open reading frames

   !/Applications/bioinfo/TransDecoder-4.0.0/TransDecoder.LongOrfs \
   -t $fa \
   -S 
   

2. Optionally, identify ORFs with homology to known proteins via blast (Mox)

#!/bin/bash
## Job Name
#SBATCH --job-name=blastx
## Allocation Definition 
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1   
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=24:00:00
## Memory per node
#SBATCH --mem=500G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/0810_1100

 
source /gscratch/srlab/programs/scripts/paths.sh

/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin/blastp \
-query \
/gscratch/srlab/sr320/data/PgenlarS-longest_orfs.pep \
-db \
/gscratch/srlab/sr320/blastdb/uniprot_sprot_080917 \
-out \
/gscratch/srlab/sr320/analyses/0810_1100/blastout \
-num_threads 28 \
-evalue 1E-05 \
-max_target_seqs 1 \
-outfmt 6 

Blastout: http://owl.fish.washington.edu/halfshell/bu-mox/analyses/0810_1100/blastout

1. predict the likely coding regions

   !/Applications/bioinfo/TransDecoder-4.0.0/TransDecoder.Predict \
   -t $fa \
   --retain_blastp_hits blastout
   

output files explained

peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed: http://owl.fish.washington.edu/halfshell/bu-alanine-wd/17-08-10/0804_Pgen_larvae.fasta.transdecoder.pep

Linkouts:
Jupyter nb w/o stranded or blast integration - here
- corresponding Alanine wd 17-08-09
Jupyter nb w Stranded and blast integration - here
- corresponding Alanine wd 17-08-10