/gscratch/srlab/programs/TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/exclude_similar_proteins.pl 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr /gscratch/srlab/programs/TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /gscratch/srlab/programs/TransDecoder-v5.5.0/util/seq_n_baseprobs_to_loglikelihood_vals.pl 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/base_freqs.dat > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/hexamer.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/score_CDS_likelihood_all_6_frames.pl 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/hexamer.scores > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 --pfam_hits /gscratch/scrubbed/samwhite/outputs/20191220_cbai_transdecoder/pfam_out/20191220.cbai.pfam.domtblout --blast_hits /gscratch/scrubbed/samwhite/outputs/20191220_cbai_transdecoder/blastp_out/20191220.cbai.blastp.outfmt6 > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/train_start_PWM.pl --transcripts /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta --selected_orfs 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/start_refinement /gscratch/srlab/programs/TransDecoder-v5.5.0/util/start_codon_refinement.pl --transcripts /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta --gff3_file 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir 20191218.C_bairdi.Trinity.fasta.transdecoder_dir > 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 cp 20191218.C_bairdi.Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 20191218.C_bairdi.Trinity.fasta.transdecoder.gff3 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_bed.pl 20191218.C_bairdi.Trinity.fasta.transdecoder.gff3 > 20191218.C_bairdi.Trinity.fasta.transdecoder.bed /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 20191218.C_bairdi.Trinity.fasta.transdecoder.gff3 --fasta /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta --genetic_code Universal > 20191218.C_bairdi.Trinity.fasta.transdecoder.pep /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 20191218.C_bairdi.Trinity.fasta.transdecoder.gff3 --fasta /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta --seqType CDS --genetic_code Universal > 20191218.C_bairdi.Trinity.fasta.transdecoder.cds