/gscratch/srlab/programs/TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/exclude_similar_proteins.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > 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 Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > 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 Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest Trinity.fasta.transdecoder_dir/base_freqs.dat > Trinity.fasta.transdecoder_dir/hexamer.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/score_CDS_likelihood_all_6_frames.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds Trinity.fasta.transdecoder_dir/hexamer.scores > Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits /gscratch/scrubbed/samwhite/outputs/20190318_transdecoder_geoduck_gonad_01_RNAseq/pfam_out/pfam.domtblout --blast_hits /gscratch/scrubbed/samwhite/outputs/20190318_transdecoder_geoduck_gonad_01_RNAseq/blastp_out/blastp.outfmt6 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/train_start_PWM.pl --transcripts /gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_gonad_01_RNAseq/trinity_out_dir/Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement /gscratch/srlab/programs/TransDecoder-v5.5.0/util/start_codon_refinement.pl --transcripts /gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_gonad_01_RNAseq/trinity_out_dir/Trinity.fasta --gff3_file Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir Trinity.fasta.transdecoder_dir > Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 cp Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Trinity.fasta.transdecoder.gff3 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_bed.pl Trinity.fasta.transdecoder.gff3 > Trinity.fasta.transdecoder.bed /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 Trinity.fasta.transdecoder.gff3 --fasta /gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_gonad_01_RNAseq/trinity_out_dir/Trinity.fasta --genetic_code Universal > Trinity.fasta.transdecoder.pep /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 Trinity.fasta.transdecoder.gff3 --fasta /gscratch/scrubbed/samwhite/outputs/20190215_trinity_geoduck_gonad_01_RNAseq/trinity_out_dir/Trinity.fasta --seqType CDS --genetic_code Universal > Trinity.fasta.transdecoder.cds