/gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/build_atgPWM_+-.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 --pwm_left 20 --pwm_right 10 /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/feature_scores_to_ROC.pl Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/plot_ROC.Rscript Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/compute_AUC.pl Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/deplete_feature_noise.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix Trinity.fasta.transdecoder_dir/start_refinement.enhanced /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/feature_scores_to_ROC.pl Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/plot_ROC.Rscript Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/compute_AUC.pl Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc /gscratch/srlab/programs/TransDecoder-v5.5.0/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || :