Index of /kundaje/marinovg/oak/programs/trinityrnaseq-Trinity-v2.8.4/util/misc

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[TXT]trinity_trans_matrix_to_rep_trans_gene_matrix.pl2018-09-12 10:08 1.7K 
[TXT]trinity_component_distribution.pl2018-09-12 10:08 2.2K 
[TXT]transdecoder_pep_to_false_fusion_finder.pl2018-09-12 10:08 1.5K 
[TXT]transcript_gff3_to_bed.pl2018-09-12 10:08 2.0K 
[TXT]transcript_fasta_to_ORF_pics.pl2018-09-12 10:08 5.7K 
[TXT]transcript_coverage_UTR_trimmer.pl2018-09-12 10:08 4.5K 
[TXT]testUnlimitStacksize.pl2018-09-12 10:08 1.8K 
[TXT]tblastn_wrapper.pl2018-09-12 10:08 628  
[TXT]tab_to_fasta.pl2018-09-12 10:08 278  
[TXT]tab_to_fastQ.pl2018-09-12 10:08 282  
[TXT]strip_fasta_header.pl2018-09-12 10:08 442  
[DIR]splice_path_analysis/2018-09-12 10:08 -  
[TXT]sort_fastq.pl2018-09-12 10:08 1.2K 
[TXT]sixFrameTranslation.pl2018-09-12 10:08 780  
[TXT]simulate_reads_sam_and_fa.pl2018-09-12 10:08 23K 
[TXT]simulate_illuminaPE_from_transcripts.wgsim.pl2018-09-12 10:08 4.0K 
[TXT]simulate_illuminaPE_from_transcripts.pl2018-09-12 10:08 9.1K 
[DIR]sim_test_framework/2018-09-12 10:08 -  
[TXT]shuffle.pl2018-09-12 10:08 212  
[TXT]run_trimmomatic_qual_trimming.pl2018-09-12 10:08 2.1K 
[TXT]run_read_simulator_per_gene.pl2018-09-12 10:08 2.1K 
[TXT]run_read_simulator_per_fasta_entry.pl2018-09-12 10:08 1.7K 
[TXT]run_jellyfish.pl2018-09-12 10:08 1.4K 
[TXT]run_bwasw_trinity.pl2018-09-12 10:08 1.1K 
[TXT]run_bwa.pl2018-09-12 10:08 3.2K 
[TXT]run_bowtie2.pl2018-09-12 10:08 1.8K 
[TXT]run_TOPHAT.pl2018-09-12 10:08 1.8K 
[TXT]run_STAR_via_samples_file.pl2018-09-12 10:08 5.4K 
[TXT]run_STAR.pl2018-09-12 10:08 5.0K 
[TXT]run_HiCpipe_bowtie.pl2018-09-12 10:08 1.2K 
[TXT]run_HISAT2_via_samples_file.pl2018-09-12 10:08 3.9K 
[TXT]run_HISAT.pl2018-09-12 10:08 4.8K 
[TXT]run_GSNAP.pl2018-09-12 10:08 4.2K 
[TXT]run_DETONATE.pl2018-09-12 10:08 2.3K 
[TXT]row_to_column.pl2018-09-12 10:08 306  
[TXT]remove_cntrl_chars.pl2018-09-12 10:08 105  
[TXT]randomly_mutate_seqs.pl2018-09-12 10:08 4.1K 
[TXT]prop_pair_sam_refiner.pl2018-09-12 10:08 1.9K 
[TXT]process_GMAP_alignments_gff3_chimeras_ok.pl2018-09-12 10:08 2.4K 
[TXT]print_kmers.pl2018-09-12 10:08 640  
[TXT]print.pl2018-09-12 10:08 867  
[ ]plot_strand_specificity_dist_by_quantile.Rscript2018-09-12 10:08 5.2K 
[TXT]plot_expressed_gene_dist.pl2018-09-12 10:08 857  
[ ]plot_ExN50_statistic.Rscript2018-09-12 10:08 387  
[TXT]pairwise_kmer_content_comparer.pl2018-09-12 10:08 1.8K 
[TXT]pair_up_fastq_files_R1_R2.pl2018-09-12 10:08 606  
[TXT]pair_up_fastq_files_LeftRight.pl2018-09-12 10:08 584  
[TXT]pair_up_fastq_files_1_2.pl2018-09-12 10:08 491  
[TXT]organize_data_table_by_trinity_component.pl2018-09-12 10:08 439  
[TXT]omp_iworm_thread_contigs_to_fa.pl2018-09-12 10:08 556  
[TXT]nameSorted_SAM_to_paired_fastq.pl2018-09-12 10:08 4.0K 
[TXT]nameSorted_SAM_to_FastQ.pl2018-09-12 10:08 1.7K 
[TXT]mpi_iworm_proc_contigs_to_fa.pl2018-09-12 10:08 358  
[TXT]merge_rsem_n_express_for_compare.pl2018-09-12 10:08 1.9K 
[TXT]merge_blast_n_rsem_results.pl2018-09-12 10:08 1.4K 
[TXT]merge_RSEM_output_to_matrix.pl2018-09-12 10:08 3.0K 
[TXT]map_gtf_transcripts_to_genome_annots.pl2018-09-12 10:08 16K 
[TXT]m8_blastclust.pl2018-09-12 10:08 6.4K 
[TXT]kmer_counter.pl2018-09-12 10:08 1.0K 
[TXT]join_expr_vals_single_table.pl2018-09-12 10:08 929  
[TXT]join_by_left_col.pl2018-09-12 10:08 827  
[TXT]join_any.pl2018-09-12 10:08 828  
[TXT]jaccard_sam_pair_refiner.pl2018-09-12 10:08 2.7K 
[TXT]iworm_welds_to_dot.pl2018-09-12 10:08 575  
[DIR]iso_reco_analysis/2018-09-12 10:08 -  
[DIR]insilico_norm_kmer_hists/2018-09-12 10:08 -  
[TXT]illustrate_ref_comparison.pl2018-09-12 10:08 4.7K 
[TXT]identify_distal_isoform_variations.pl2018-09-12 10:08 4.6K 
[TXT]hicpipe_raw_converter.pl2018-09-12 10:08 353  
[TXT]gtf_to_introns.pl2018-09-12 10:08 3.0K 
[TXT]gtf_to_bed_format.pl2018-09-12 10:08 1.8K 
[TXT]gmap_native_to_format_converter.pl2018-09-12 10:08 1.9K 
[TXT]gmap_gff3_to_percent_length_stats.pl2018-09-12 10:08 1.8K 
[TXT]gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl2018-09-12 10:08 1.0K 
[TXT]gmap_gff3_chimera_jaccard_analyzer.pl2018-09-12 10:08 4.7K 
[TXT]gff3_to_genome_feature_base_encoding.pl2018-09-12 10:08 2.5K 
[TXT]gff3_to_genome_feature_base_encoding.parse_SAM.pl2018-09-12 10:08 4.5K 
[TXT]gff3_file_utr_coverage_trimmer.pl2018-09-12 10:08 6.7K 
[TXT]gff3_file_to_cdna.pl2018-09-12 10:08 3.0K 
[TXT]get_welds_from_chrysals_graphFromFasta_out.pl2018-09-12 10:08 391  
[TXT]get_path_nodes_from_fasta.pl2018-09-12 10:08 647  
[TXT]get_longest_isoform_seq_per_trinity_gene.pl2018-09-12 10:08 1.7K 
[TXT]get_GC_content_dist.pl2018-09-12 10:08 1.5K 
[TXT]genome_gff3_to_gene_gff3_partitions.pl2018-09-12 10:08 3.1K 
[TXT]gene_to_shared_transcript_content.pl2018-09-12 10:08 2.0K 
[TXT]gene_gff3_to_introns.pl2018-09-12 10:08 1.9K 
[TXT]frag_to_bed.pl2018-09-12 10:08 483  
[TXT]frag_boundary_to_wig.pl2018-09-12 10:08 1.2K 
[TXT]flattened_gff_n_genome_to_Trinity_emulator.pl2018-09-12 10:08 4.5K 
[TXT]filter_similar_seqs_expr_and_strand_aware.pl2018-09-12 10:08 7.8K 
[TXT]filter_out_accs_from_fasta.pl2018-09-12 10:08 1.1K 
[TXT]fastq_unweave_pairs.pl2018-09-12 10:08 1.2K 
[TXT]fastq_stats.pl2018-09-12 10:08 6.6K 
[TXT]fastq_merge_sorted_tab_lists.pl2018-09-12 10:08 2.1K 
[TXT]fastq_interleave_pairs.pl2018-09-12 10:08 1.3K 
[TXT]fastq_cleaner.pl2018-09-12 10:08 1.5K 
[TXT]fasta_write_sense_n_anti.pl2018-09-12 10:08 632  
[TXT]fasta_to_cmd_generator.pl2018-09-12 10:08 3.2K 
[TXT]fasta_seq_length.pl2018-09-12 10:08 509  
[TXT]fasta_remove_duplicates.pl2018-09-12 10:08 679  
[TXT]fasta_filter_by_min_length.pl2018-09-12 10:08 558  
[TXT]fasta_file_reformatter.pl2018-09-12 10:08 464  
[TXT]fastQ_top_N_records.pl2018-09-12 10:08 644  
[TXT]fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl2018-09-12 10:08 3.3K 
[TXT]fastQ_rand_subset.pl2018-09-12 10:08 2.7K 
[TXT]fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl2018-09-12 10:08 2.4K 
[TXT]fastQ_append_acc.pl2018-09-12 10:08 739  
[TXT]fan_out_fasta_seqs_to_indiv_files.pl2018-09-12 10:08 2.6K 
[TXT]extract_fastQ_pairings.pl2018-09-12 10:08 6.5K 
[TXT]examine_weldmer_halves.pl2018-09-12 10:08 2.3K 
[TXT]examine_strand_specificity.pl2018-09-12 10:08 2.7K 
[TXT]examine_iworm_FL_across_threads.pl2018-09-12 10:08 2.4K 
[TXT]ensure_paired_end_bam_file.pl2018-09-12 10:08 936  
[TXT]determine_RF_strand_specificity.pl2018-09-12 10:08 2.4K 
[TXT]describe_SAM_read_flag_info.pl2018-09-12 10:08 2.0K 
[TXT]decode_SAM_flag_value.pl2018-09-12 10:08 1.6K 
[TXT]count_trans_per_component.pl2018-09-12 10:08 1.1K 
[TXT]count_number_fasta_seqs.pl2018-09-12 10:08 348  
[TXT]count_matrix_features_given_MIN_TPM_threshold.pl2018-09-12 10:08 877  
[TXT]count_iso_per_gene_dist.pl2018-09-12 10:08 668  
[TXT]count_features_given_MIN_FPKM_threshold.pl2018-09-12 10:08 769  
[TXT]count_N50_given_MIN_FPKM_threshold.pl2018-09-12 10:08 1.7K 
[TXT]convert_fasta_identifiers_for_FL_analysis.pl2018-09-12 10:08 685  
[TXT]contig_ExN50_statistic.pl2018-09-12 10:08 3.0K 
[TXT]component_to_graph_dot.pl2018-09-12 10:08 4.0K 
[TXT]compare_bflies.pl2018-09-12 10:08 1.9K 
[TXT]compare_FL_stats.pl2018-09-12 10:08 1.5K 
[TXT]combined_nameSorted_to_dup_pairs_removed.pl2018-09-12 10:08 2.7K 
[TXT]chrys_graph_to_dot.pl2018-09-12 10:08 492  
[TXT]check_fastQ_pair_ordering.pl2018-09-12 10:08 1.4K 
[TXT]check_chrysalis_graph_reciprocal_edges.pl2018-09-12 10:08 1.0K 
[TXT]cdna_fasta_file_to_transcript_gtf.pl2018-09-12 10:08 768  
[TXT]cdhit_examine_isoforms.pl2018-09-12 10:08 1.3K 
[TXT]cat_require_newlines.pl2018-09-12 10:08 223  
[TXT]capture_orig_n_unmapped_reads.pl2018-09-12 10:08 5.5K 
[DIR]blat_util/2018-09-12 10:08 -  
[TXT]blastn_wrapper.pl2018-09-12 10:08 627  
[TXT]blast_outfmt6_group_segments.tophit_coverage.pl2018-09-12 10:08 3.0K 
[TXT]blast_outfmt6_group_segments.to_Markov_Clustering.pl2018-09-12 10:08 4.3K 
[TXT]blast_outfmt6_group_segments.pl2018-09-12 10:08 4.8K 
[DIR]bam_gene_tests/2018-09-12 10:08 -  
[TXT]average.pl2018-09-12 10:08 804  
[TXT]analyze_blastPlus_topHit_coverage.org_matrix.pl2018-09-12 10:08 1.2K 
[TXT]analyze_blastPlus_topHit_coverage.extract_OS.pl2018-09-12 10:08 2.1K 
[TXT]analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl2018-09-12 10:08 5.9K 
[TXT]analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl2018-09-12 10:08 2.6K 
[DIR]altsplice_simulation_toolkit/2018-09-12 10:08 -  
[DIR]alt_GG_read_partitioning_JCornish/2018-09-12 10:08 -  
[TXT]allele_simulator.pl2018-09-12 10:08 2.1K 
[TXT]align_reads_launch_igv.pl2018-09-12 10:08 1.2K 
[TXT]alexie_analyze_blast.pl2018-09-12 10:08 35K 
[TXT]acc_list_to_fasta_entries.pl2018-09-12 10:08 4.5K 
[TXT]Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl2018-09-12 10:08 9.4K 
[TXT]TophatCufflinksWrapper.pl2018-09-12 10:08 4.8K 
[TXT]TPM_weighted_gene_length.py2018-09-12 10:08 4.6K 
[DIR]TEST_SUPPORT/2018-09-12 10:08 -  
[TXT]SRA_to_fastq.pl2018-09-12 10:08 1.6K 
[ ]SRA_to_fastq.notes2018-09-12 10:08 77  
[TXT]SAM_to_fasta.pl2018-09-12 10:08 700  
[TXT]SAM_to_bed.pl2018-09-12 10:08 1.5K 
[TXT]SAM_toString.pl2018-09-12 10:08 1.0K 
[TXT]SAM_sortAny_to_count_stats.pl2018-09-12 10:08 4.3K 
[TXT]SAM_show_alignment.summarize_stats.pl2018-09-12 10:08 4.0K 
[TXT]SAM_show_alignment.pl2018-09-12 10:08 7.4K 
[TXT]SAM_pair_to_bed.pl2018-09-12 10:08 1.9K 
[TXT]SAM_nameSorted_to_uniq_count_stats.pl2018-09-12 10:08 7.5K 
[TXT]SAM_intron_extractor.pl2018-09-12 10:08 3.5K 
[TXT]SAM_coordsorted_max_reads_per_position.pl2018-09-12 10:08 1.0K 
[DIR]PerlLib/2018-09-12 10:08 -  
[TXT]N50.pl2018-09-12 10:08 895  
[DIR]Monarch_util/2018-09-12 10:08 -  
[ ]Monarch2018-09-12 10:08 8.7K 
[TXT]HiCpipe_nameSortedSam_to_raw.pl2018-09-12 10:08 2.3K 
[TXT]ButterflyFastaToGraphDot.pl2018-09-12 10:08 1.7K 
[TXT]BLAT_to_SAM.pl2018-09-12 10:08 21K 
[DIR]Artemis/2018-09-12 10:08 -  
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