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bin/util/misc/PerlLib/SegmentGraph.pm
bin/util/misc/SAM_coordsorted_max_reads_per_position.pl
bin/util/misc/SAM_intron_extractor.pl
bin/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
bin/util/misc/SAM_pair_to_bed.pl
bin/util/misc/SAM_show_alignment.pl
bin/util/misc/SAM_show_alignment.summarize_stats.pl
bin/util/misc/SAM_sortAny_to_count_stats.pl
bin/util/misc/SAM_toString.pl
bin/util/misc/SAM_to_bed.pl
bin/util/misc/SAM_to_fasta.pl
bin/util/misc/SAM_to_gff3.minimap2.pl
bin/util/misc/SRA_to_fastq.notes
bin/util/misc/SRA_to_fastq.pl
bin/util/misc/STAR_align_log_parser.py
bin/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
bin/util/misc/TPM_weighted_gene_length.py
bin/util/misc/TophatCufflinksWrapper.pl
bin/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
bin/util/misc/Trinity_node_seq_extractor.pl
bin/util/misc/acc_list_to_fasta_entries.pl
bin/util/misc/alexie_analyze_blast.pl
bin/util/misc/align_reads_launch_igv.pl
bin/util/misc/allele_simulator.pl
bin/util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
bin/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
bin/util/misc/altsplice_simulation_toolkit/sim_single_bubble.pl
bin/util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
bin/util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
bin/util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
bin/util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
bin/util/misc/average.pl
bin/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
bin/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
bin/util/misc/bam_gene_tests/harvest_transcripts.pl
bin/util/misc/bam_gene_tests/write_trin_cmds.pl
bin/util/misc/blast_outfmt6_group_segments.pl
bin/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
bin/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
bin/util/misc/blastn_wrapper.pl
bin/util/misc/blat_util/blat_sam_add_reads2.pl
bin/util/misc/blat_util/blat_to_sam.pl
bin/util/misc/blat_util/blat_top_hit_extractor.pl
bin/util/misc/blat_util/process_BLAT_alignments.pl
bin/util/misc/blat_util/pslx_to_gff3.pl
bin/util/misc/blat_util/run_BLAT_shortReads.pl
bin/util/misc/blat_util/top_blat_sam_extractor.pl
bin/util/misc/capture_orig_n_unmapped_reads.pl
bin/util/misc/cat_require_newlines.pl
bin/util/misc/cdhit_examine_isoforms.pl
bin/util/misc/cdna_fasta_file_to_transcript_gtf.pl
bin/util/misc/check_chrysalis_graph_reciprocal_edges.pl
bin/util/misc/check_fastQ_pair_ordering.pl
bin/util/misc/chrys_graph_to_dot.pl
bin/util/misc/collate_fqs.pl
bin/util/misc/combined_nameSorted_to_dup_pairs_removed.pl
bin/util/misc/compare_FL_stats.pl
bin/util/misc/compare_bflies.pl
bin/util/misc/component_to_graph_dot.pl
bin/util/misc/contig_ExN50_statistic.pl
bin/util/misc/convert_fasta_identifiers_for_FL_analysis.pl
bin/util/misc/count_N50_given_MIN_FPKM_threshold.pl
bin/util/misc/count_features_given_MIN_FPKM_threshold.pl
bin/util/misc/count_iso_per_gene_dist.pl
bin/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
bin/util/misc/count_number_fasta_seqs.pl
bin/util/misc/count_trans_per_component.pl
bin/util/misc/decode_SAM_flag_value.pl
bin/util/misc/describe_SAM_read_flag_info.pl
bin/util/misc/determine_RF_strand_specificity.pl
bin/util/misc/ensure_paired_end_bam_file.pl
bin/util/misc/examine_iworm_FL_across_threads.pl
bin/util/misc/examine_strand_specificity.pl
bin/util/misc/examine_weldmer_halves.pl
bin/util/misc/extract_fastQ_pairings.pl
bin/util/misc/fan_out_fasta_seqs_to_indiv_files.pl
bin/util/misc/fastQ_append_acc.pl
bin/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
bin/util/misc/fastQ_rand_subset.pl
bin/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
bin/util/misc/fastQ_top_N_records.pl
bin/util/misc/fasta_file_reformatter.pl
bin/util/misc/fasta_filter_by_min_length.pl
bin/util/misc/fasta_remove_duplicates.pl
bin/util/misc/fasta_seq_length.pl
bin/util/misc/fasta_to_cmd_generator.pl
bin/util/misc/fasta_to_tab.pl
bin/util/misc/fasta_write_sense_n_anti.pl
bin/util/misc/fastq_cleaner.pl
bin/util/misc/fastq_interleave_pairs.pl
bin/util/misc/fastq_merge_sorted_tab_lists.pl
bin/util/misc/fastq_stats.pl
bin/util/misc/fastq_unweave_pairs.pl
bin/util/misc/filter_out_accs_from_fasta.pl
bin/util/misc/filter_similar_seqs_expr_and_strand_aware.pl
bin/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
bin/util/misc/frag_boundary_to_wig.pl
bin/util/misc/frag_to_bed.pl
bin/util/misc/gene_gff3_to_introns.pl
bin/util/misc/gene_to_shared_transcript_content.pl
bin/util/misc/genome_gff3_to_gene_gff3_partitions.pl
bin/util/misc/get_GC_content_dist.pl
bin/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
bin/util/misc/get_path_nodes_from_fasta.pl
bin/util/misc/get_welds_from_chrysals_graphFromFasta_out.pl
bin/util/misc/gff3_file_to_cdna.pl
bin/util/misc/gff3_file_utr_coverage_trimmer.pl
bin/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
bin/util/misc/gff3_to_genome_feature_base_encoding.pl
bin/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
bin/util/misc/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
bin/util/misc/gmap_gff3_to_percent_length_stats.pl
bin/util/misc/gmap_native_to_format_converter.pl
bin/util/misc/gtf_to_bed_format.pl
bin/util/misc/gtf_to_introns.pl
bin/util/misc/hicpipe_raw_converter.pl
bin/util/misc/identify_distal_isoform_variations.pl
bin/util/misc/illustrate_ref_comparison.pl
bin/util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
bin/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
bin/util/misc/insilico_norm_kmer_hists/plot_me.R
bin/util/misc/insilico_norm_kmer_hists/result.pdf
bin/util/misc/iso_reco_analysis/bam_to_cuff.pl
bin/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl
bin/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl
bin/util/misc/iso_reco_analysis/gmap_to_ref.pl
bin/util/misc/iso_reco_analysis/notes
bin/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl
bin/util/misc/iso_reco_analysis/run_trinity_no_LR.pl
bin/util/misc/iso_reco_analysis/sim_reads.pl
bin/util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl
bin/util/misc/iworm_welds_to_dot.pl
bin/util/misc/jaccard_sam_pair_refiner.pl
bin/util/misc/join_any.pl
bin/util/misc/join_by_left_col.pl
bin/util/misc/join_expr_vals_single_table.pl
bin/util/misc/kmer_counter.pl
bin/util/misc/m8_blastclust.pl
bin/util/misc/map_gtf_transcripts_to_genome_annots.pl
bin/util/misc/merge_RSEM_output_to_matrix.pl
bin/util/misc/merge_blast_n_rsem_results.pl
bin/util/misc/merge_replicate_bams_via_samples_file.pl
bin/util/misc/merge_rsem_n_express_for_compare.pl
bin/util/misc/mpi_iworm_proc_contigs_to_fa.pl
bin/util/misc/nameSorted_SAM_to_FastQ.pl
bin/util/misc/nameSorted_SAM_to_paired_fastq.pl
bin/util/misc/omp_iworm_thread_contigs_to_fa.pl
bin/util/misc/organize_data_table_by_trinity_component.pl
bin/util/misc/pair_up_fastq_files_1_2.pl
bin/util/misc/pair_up_fastq_files_LeftRight.pl
bin/util/misc/pair_up_fastq_files_R1_R2.pl
bin/util/misc/pairwise_kmer_content_comparer.pl
bin/util/misc/plot_ExN50_statistic.Rscript
bin/util/misc/plot_expressed_gene_dist.pl
bin/util/misc/plot_strand_specificity_dist_by_quantile.Rscript
bin/util/misc/print.pl
bin/util/misc/print_kmers.pl
bin/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
bin/util/misc/process_minimap2_alignments.pl
bin/util/misc/prop_pair_sam_refiner.pl
bin/util/misc/randomly_mutate_seqs.pl
bin/util/misc/randomly_sample_PE_fastq.pl
bin/util/misc/remove_cntrl_chars.pl
bin/util/misc/rename_fasta_accessions_using_Trinotate_annot_mappings.pl
bin/util/misc/row_to_column.pl
bin/util/misc/run_DETONATE.pl
bin/util/misc/run_GSNAP.pl
bin/util/misc/run_HISAT.pl
bin/util/misc/run_HISAT2_via_samples_file.pl
bin/util/misc/run_HiCpipe_bowtie.pl
bin/util/misc/run_STAR.pl
bin/util/misc/run_STAR_via_samples_file.pl
bin/util/misc/run_Stringtie_via_bam_file_list.pl
bin/util/misc/run_TOPHAT.pl
bin/util/misc/run_bowtie2.pl
bin/util/misc/run_bwa.pl
bin/util/misc/run_bwasw_trinity.pl
bin/util/misc/run_jellyfish.pl
bin/util/misc/run_read_simulator_per_fasta_entry.pl
bin/util/misc/run_read_simulator_per_gene.pl
bin/util/misc/run_trimmomatic_qual_trimming.pl
bin/util/misc/seqinfo_refseq_to_dot.pl
bin/util/misc/shuffle.pl
bin/util/misc/sim_test_framework/audit_summary_stats.pl
bin/util/misc/sim_test_framework/audit_summary_stats.reexamine.pl
bin/util/misc/sim_test_framework/info_files_to_eval_cmds.pl
bin/util/misc/sim_test_framework/partition_target_transcripts.pl
bin/util/misc/sim_test_framework/run_Trinity_eval.pl
bin/util/misc/sim_test_framework/run_Trinity_eval.sh
bin/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
bin/util/misc/sim_test_framework/util/find_pruned_edges_shouldve_kept.pl
bin/util/misc/sim_test_framework/write_simulate_read_commands.pl
bin/util/misc/simulate_illuminaPE_from_transcripts.pl
bin/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
bin/util/misc/simulate_reads_sam_and_fa.pl
bin/util/misc/sixFrameTranslation.pl
bin/util/misc/sort_fastq.pl
bin/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
bin/util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl
bin/util/misc/splice_path_analysis/diff_splice_paths.pl
bin/util/misc/splice_path_analysis/intron_barcharter.pl
bin/util/misc/strip_fasta_header.pl
bin/util/misc/tab_to_fastQ.pl
bin/util/misc/tab_to_fasta.pl
bin/util/misc/tblastn_wrapper.pl
bin/util/misc/testUnlimitStacksize.pl
bin/util/misc/transcript_coverage_UTR_trimmer.pl
bin/util/misc/transcript_fasta_to_ORF_pics.pl
bin/util/misc/transcript_gff3_to_bed.pl
bin/util/misc/transdecoder_pep_to_false_fusion_finder.pl
bin/util/misc/trinity_component_distribution.pl
bin/util/misc/trinity_trans_matrix_to_rep_trans_gene_matrix.pl
bin/util/misc/try_estimate_TPM_filtering_threshold.Rscript
bin/util/misc/validate_fastqs.py
bin/util/retrieve_sequences_from_fasta.pl
bin/util/sift_bam_max_cov.pl
bin/util/support_scripts/ExitTester.jar
bin/util/support_scripts/GG_partitioned_trinity_aggregator.pl
bin/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
bin/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
bin/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
bin/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
bin/util/support_scripts/SAM_filter_out_unmapped_reads.pl
bin/util/support_scripts/SAM_ordered_pair_jaccard.pl
bin/util/support_scripts/SAM_set_transcribed_orient_info.pl
bin/util/support_scripts/SAM_strand_separator.pl
bin/util/support_scripts/SAM_to_frag_coords.pl
bin/util/support_scripts/add_LR_reads_to_iworm_bundle.pl
bin/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl
bin/util/support_scripts/batch_cmds.pl
bin/util/support_scripts/bowtie2_wrapper.pl
bin/util/support_scripts/define_SAM_coverage_partitions2.pl
bin/util/support_scripts/define_coverage_partitions.pl
bin/util/support_scripts/eXpress_trans_to_gene_results.pl
bin/util/support_scripts/ensure_coord_sorted_sam.pl
bin/util/support_scripts/extract_reads_per_partition.pl
bin/util/support_scripts/fastQ_to_fastA.pl
bin/util/support_scripts/fastQ_to_tab.pl
bin/util/support_scripts/fasta_find_duplicates.pl
bin/util/support_scripts/fasta_to_tab.pl
bin/util/support_scripts/filter_iworm_by_min_length_or_cov.pl
bin/util/support_scripts/filter_transcripts_require_min_cov.pl
bin/util/support_scripts/fragment_coverage_writer.pl
bin/util/support_scripts/get_Trinity_gene_to_trans_map.pl
bin/util/support_scripts/inchworm_transcript_splitter.pl
bin/util/support_scripts/iworm_LR_to_scaff_pairs.pl
bin/util/support_scripts/jaccard_fasta_clipper.pl
bin/util/support_scripts/jaccard_wig_clipper.pl
bin/util/support_scripts/join_partitions_within_range.pl
bin/util/support_scripts/kallisto_trans_to_gene_results.pl
bin/util/support_scripts/merge_pair_and_LR_scaff_links.pl
bin/util/support_scripts/nbkc_merge_left_right_stats.pl
bin/util/support_scripts/nbkc_normalize.pl
bin/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
bin/util/support_scripts/outfmt6_add_percent_match_length.pl
bin/util/support_scripts/partition_chrysalis_graphs_n_reads.pl
bin/util/support_scripts/partitioned_trinity_aggregator.pl
bin/util/support_scripts/plugin_install_tests.sh
bin/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
bin/util/support_scripts/print_butterfly_assemblies.pl
bin/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
bin/util/support_scripts/revcomp_fasta.pl
bin/util/support_scripts/run_TMM_scale_matrix.pl
bin/util/support_scripts/run_UpperQuartileNormalization_matrix.Rscript
bin/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
bin/util/support_scripts/salmon_runner.pl
bin/util/support_scripts/salmon_trans_to_gene_results.pl
bin/util/support_scripts/scaffold_iworm_contigs.pl
bin/util/support_scripts/segment_GFF_partitions.pl
bin/util/support_scripts/tests/sample_data_tests.py
bin/util/support_scripts/tests/test_prep.py
bin/util/support_scripts/tests/tests.py
bin/util/support_scripts/trinity_install_tests.sh
bin/util/support_scripts/trinity_installer.py
bin/util/support_scripts/wig_clip_to_bed.pl
bin/util/support_scripts/write_partitioned_trinity_cmds.pl
etc/conda/activate.d/trinity-2.15.2.sh
etc/conda/deactivate.d/trinity-2.15.2.sh
