/gscratch/srlab/programs/TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/exclude_similar_proteins.pl hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr /gscratch/srlab/programs/TransDecoder-v5.5.0/util/get_top_longest_fasta_entries.pl hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest /gscratch/srlab/programs/TransDecoder-v5.5.0/util/seq_n_baseprobs_to_loglikelihood_vals.pl hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest hemat_transcriptome_v1.7.fasta.transdecoder_dir/base_freqs.dat > hemat_transcriptome_v1.7.fasta.transdecoder_dir/hexamer.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/score_CDS_likelihood_all_6_frames.pl hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds hemat_transcriptome_v1.7.fasta.transdecoder_dir/hexamer.scores > hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/select_best_ORFs_per_transcript.pl --gff3_file hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 797 --pfam_hits 20210309_hemat_transcriptome_v1.7.fasta.pfam_out/20210309_hemat_transcriptome_v1.7.fasta.pfam.domtblout --blast_hits 20210309_hemat_transcriptome_v1.7.fasta.blastp_out/20210309_hemat_transcriptome_v1.7.fasta.blastp.outfmt6 > hemat_transcriptome_v1.7.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/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta --selected_orfs hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix hemat_transcriptome_v1.7.fasta.transdecoder_dir/start_refinement /gscratch/srlab/programs/TransDecoder-v5.5.0/util/start_codon_refinement.pl --transcripts /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta --gff3_file hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 --workdir hemat_transcriptome_v1.7.fasta.transdecoder_dir > hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 cp hemat_transcriptome_v1.7.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 hemat_transcriptome_v1.7.fasta.transdecoder.gff3 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_bed.pl hemat_transcriptome_v1.7.fasta.transdecoder.gff3 > hemat_transcriptome_v1.7.fasta.transdecoder.bed /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 hemat_transcriptome_v1.7.fasta.transdecoder.gff3 --fasta /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta --genetic_code Universal > hemat_transcriptome_v1.7.fasta.transdecoder.pep /gscratch/srlab/programs/TransDecoder-v5.5.0/util/gff3_file_to_proteins.pl --gff3 hemat_transcriptome_v1.7.fasta.transdecoder.gff3 --fasta /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta --seqType CDS --genetic_code Universal > hemat_transcriptome_v1.7.fasta.transdecoder.cds