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-rw-r--r-- | 88 | 00README | blob | raw |
-rwxr-xr-x | 3552 | BGB_delete_track | blob | raw |
-rwxr-xr-x | 4495 | BGB_intersect | blob | raw |
-rwxr-xr-x | 3877 | BGB_list | blob | raw |
-rwxr-xr-x | 3774 | BGB_read_track | blob | raw |
-rwxr-xr-x | 6593 | BGB_upload | blob | raw |
-rwxr-xr-x | 2531 | add_ident | blob | raw |
-rwxr-xr-x | 1897 | align_pair_seq | blob | raw |
-rwxr-xr-x | 2683 | align_seq | blob | raw |
-rwxr-xr-x | 3309 | analyze_assembly | blob | raw |
-rwxr-xr-x | 2021 | analyze_bed | blob | raw |
-rwxr-xr-x | 2220 | analyze_gc | blob | raw |
-rwxr-xr-x | 2042 | analyze_seq | blob | raw |
-rwxr-xr-x | 3860 | analyze_snp | blob | raw |
-rwxr-xr-x | 2794 | analyze_tags | blob | raw |
-rwxr-xr-x | 5441 | analyze_vals | blob | raw |
-rwxr-xr-x | 5854 | assemble_contigs | blob | raw |
-rwxr-xr-x | 3224 | assemble_pairs | blob | raw |
-rwxr-xr-x | 3874 | assemble_seq_idba | blob | raw |
-rwxr-xr-x | 5113 | assemble_seq_ray | blob | raw |
-rwxr-xr-x | 5913 | assemble_seq_velvet | blob | raw |
-rwxr-xr-x | 4041 | assemble_tag_contigs | blob | raw |
-rwxr-xr-x | 1995 | bin_vals | blob | raw |
-rwxr-xr-x | 2200 | bioscript | blob | raw |
-rwxr-xr-x | 5761 | biostat | blob | raw |
-rwxr-xr-x | 9504 | blast_seq | blob | raw |
-rwxr-xr-x | 6086 | blast_seq_pair | blob | raw |
-rwxr-xr-x | 5783 | blat_seq | blob | raw |
-rwxr-xr-x | 3698 | bowtie2_seq | blob | raw |
-rwxr-xr-x | 6717 | bowtie_seq | blob | raw |
-rwxr-xr-x | 3839 | bwa_seq | blob | raw |
-rwxr-xr-x | 2222 | calc_N50 | blob | raw |
-rwxr-xr-x | 2809 | calc_bit_scores | blob | raw |
lrwxrwxrwx | 33 | calc_density -> ../code_python/Cjung/calc_density | blob | raw |
-rwxr-xr-x | 3548 | calc_fixedstep | blob | raw |
-rwxr-xr-x | 2137 | cat_seq | blob | raw |
-rwxr-xr-x | 6179 | classify_taxonomy | blob | raw |
-rwxr-xr-x | 2091 | clip_adaptor | blob | raw |
-rwxr-xr-x | 2044 | clip_seq | blob | raw |
-rwxr-xr-x | 2281 | complement_seq | blob | raw |
-rwxr-xr-x | 3165 | compute | blob | raw |
-rwxr-xr-x | 2640 | count_records | blob | raw |
-rwxr-xr-x | 3549 | count_vals | blob | raw |
-rwxr-xr-x | 3419 | create_blast_index | blob | raw |
-rwxr-xr-x | 2566 | create_bowtie2_index | blob | raw |
-rwxr-xr-x | 3067 | create_bowtie_index | blob | raw |
-rwxr-xr-x | 3049 | create_bwa_index | blob | raw |
-rwxr-xr-x | 3172 | create_fixedstep_index | blob | raw |
-rwxr-xr-x | 2996 | create_seq_index | blob | raw |
-rwxr-xr-x | 3187 | create_vmatch_index | blob | raw |
-rwxr-xr-x | 2899 | create_weight_matrix | blob | raw |
-rwxr-xr-x | 4347 | denoise_seq | blob | raw |
-rwxr-xr-x | 2345 | digest_seq | blob | raw |
-rwxr-xr-x | 1832 | duplicate_record | blob | raw |
-rwxr-xr-x | 2952 | embl_index | blob | raw |
-rwxr-xr-x | 4252 | extract_seq | blob | raw |
-rwxr-xr-x | 2602 | find_SNPs | blob | raw |
-rwxr-xr-x | 6184 | find_adaptor | blob | raw |
-rwxr-xr-x | 10011 | find_barcodes | blob | raw |
-rwxr-xr-x | 3353 | find_gaps | blob | raw |
-rwxr-xr-x | 2318 | find_genes | blob | raw |
-rwxr-xr-x | 1829 | find_homopolymers | blob | raw |
-rwxr-xr-x | 2797 | find_orfs | blob | raw |
-rwxr-xr-x | 2362 | find_pairs | blob | raw |
-rwxr-xr-x | 3313 | findsim_seq | blob | raw |
-rwxr-xr-x | 2399 | flip_tab | blob | raw |
-rwxr-xr-x | 2477 | fold_seq | blob | raw |
-rwxr-xr-x | 5509 | format_genome | blob | raw |
-rwxr-xr-x | 4828 | get_embl_entry | blob | raw |
-rwxr-xr-x | 5742 | get_fixedstep | blob | raw |
-rwxr-xr-x | 6184 | get_genome_align | blob | raw |
-rwxr-xr-x | 5204 | get_genome_phastcons | blob | raw |
-rwxr-xr-x | 8139 | get_genome_seq | blob | raw |
-rwxr-xr-x | 5569 | get_seq | blob | raw |
-rwxr-xr-x | 9285 | grab | blob | raw |
-rwxr-xr-x | 2148 | head_records | blob | raw |
-rwxr-xr-x | 5569 | hmmer_seq | blob | raw |
-rwxr-xr-x | 3386 | indel_seq | blob | raw |
-rwxr-xr-x | 3955 | intersect_records | blob | raw |
-rwxr-xr-x | 2542 | invert_align | blob | raw |
-rwxr-xr-x | 2069 | join_seq | blob | raw |
-rwxr-xr-x | 2174 | kmer_freq | blob | raw |
-rwxr-xr-x | 1629 | length_seq | blob | raw |
-rwxr-xr-x | 2254 | length_vals | blob | raw |
-rwxr-xr-x | 2006 | list_biopieces | blob | raw |
-rwxr-xr-x | 2425 | list_genomes | blob | raw |
-rwxr-xr-x | 2217 | list_mysql_databases | blob | raw |
lrwxrwxrwx | 34 | lowercase_seq -> ../code_python/Cjung/lowercase_seq | blob | raw |
-rwxr-xr-x | 2040 | mask_seq | blob | raw |
-rwxr-xr-x | 2858 | match_seq | blob | raw |
-rwxr-xr-x | 4273 | mate_pair_dist | blob | raw |
-rwxr-xr-x | 3740 | max_vals | blob | raw |
-rwxr-xr-x | 3740 | mean_scores | blob | raw |
-rwxr-xr-x | 3753 | mean_vals | blob | raw |
-rwxr-xr-x | 3682 | median_vals | blob | raw |
-rwxr-xr-x | 5981 | merge_records | blob | raw |
-rwxr-xr-x | 2630 | merge_vals | blob | raw |
-rwxr-xr-x | 3739 | min_vals | blob | raw |
-rwxr-xr-x | 3274 | mutate_seq | blob | raw |
-rwxr-xr-x | 2786 | oligo_freq | blob | raw |
-rwxr-xr-x | 2633 | order_pairs | blob | raw |
-rwxr-xr-x | 6488 | patscan_seq | blob | raw |
-rwxr-xr-x | 6279 | pcr_seq | blob | raw |
-rwxr-xr-x | 4450 | plot_chrdist | blob | raw |
-rwxr-xr-x | 3564 | plot_distribution | blob | raw |
-rwxr-xr-x | 3964 | plot_histogram | blob | raw |
-rwxr-xr-x | 3118 | plot_karyogram | blob | raw |
-rwxr-xr-x | 3779 | plot_lendist | blob | raw |
-rwxr-xr-x | 4585 | plot_lines | blob | raw |
-rwxr-xr-x | 7078 | plot_matches | blob | raw |
-rwxr-xr-x | 5634 | plot_nucleotide_distribution | blob | raw |
-rwxr-xr-x | 5279 | plot_phastcons_profiles | blob | raw |
-rwxr-xr-x | 4125 | plot_scores | blob | raw |
-rwxr-xr-x | 2571 | plot_seqlogo | blob | raw |
-rwxr-xr-x | 2263 | print_wiki | blob | raw |
-rwxr-xr-x | 2085 | progress_meter | blob | raw |
-rwxr-xr-x | 2994 | random_records | blob | raw |
-rwxr-xr-x | 3140 | read_2bit | blob | raw |
-rwxr-xr-x | 5082 | read_454 | blob | raw |
-rwxr-xr-x | 2786 | read_ace | blob | raw |
-rwxr-xr-x | 3078 | read_bed | blob | raw |
-rwxr-xr-x | 3757 | read_blast_tab | blob | raw |
-rwxr-xr-x | 2976 | read_embl | blob | raw |
-rwxr-xr-x | 2294 | read_fasta | blob | raw |
-rwxr-xr-x | 2967 | read_fastq | blob | raw |
-rwxr-xr-x | 2729 | read_fixedstep | blob | raw |
-rwxr-xr-x | 2976 | read_genbank | blob | raw |
-rwxr-xr-x | 2703 | read_gff | blob | raw |
-rwxr-xr-x | 2712 | read_kiss | blob | raw |
-rwxr-xr-x | 2967 | read_mysql | blob | raw |
-rwxr-xr-x | 2761 | read_psl | blob | raw |
-rwxr-xr-x | 2211 | read_sam | blob | raw |
-rwxr-xr-x | 2538 | read_sff | blob | raw |
-rwxr-xr-x | 4131 | read_soft | blob | raw |
-rwxr-xr-x | 3514 | read_solid | blob | raw |
-rwxr-xr-x | 3297 | read_stockholm | blob | raw |
-rwxr-xr-x | 4140 | read_tab | blob | raw |
-rwxr-xr-x | 2693 | read_ucsc_config | blob | raw |
-rwxr-xr-x | 4000 | remove_adaptor | blob | raw |
-rwxr-xr-x | 2390 | remove_indel_columns | blob | raw |
-rwxr-xr-x | 2033 | remove_indels | blob | raw |
-rwxr-xr-x | 2551 | remove_keys | blob | raw |
-rwxr-xr-x | 4012 | remove_mysql_tables | blob | raw |
-rwxr-xr-x | 3287 | remove_primers | blob | raw |
-rwxr-xr-x | 4974 | remove_ucsc_tracks | blob | raw |
-rwxr-xr-x | 2277 | rename_keys | blob | raw |
-rwxr-xr-x | 3453 | replace_vals | blob | raw |
-rwxr-xr-x | 3587 | rescan_seq | blob | raw |
-rwxr-xr-x | 2067 | reverse_seq | blob | raw |
-rwxr-xr-x | 2010 | scores_to_dec | blob | raw |
-rwxr-xr-x | 3059 | shred_seq | blob | raw |
-rwxr-xr-x | 1616 | shuffle_records | blob | raw |
-rwxr-xr-x | 2138 | shuffle_seq | blob | raw |
-rwxr-xr-x | 4804 | soap_seq | blob | raw |
-rwxr-xr-x | 3058 | sort_records | blob | raw |
-rwxr-xr-x | 3176 | split_bed | blob | raw |
-rwxr-xr-x | 3259 | split_seq | blob | raw |
-rwxr-xr-x | 2962 | split_vals | blob | raw |
-rwxr-xr-x | 3267 | substitute_vals | blob | raw |
-rwxr-xr-x | 3545 | sum_vals | blob | raw |
-rwxr-xr-x | 1626 | swapcase_seq | blob | raw |
-rwxr-xr-x | 2931 | tile_seq | blob | raw |
-rwxr-xr-x | 2707 | translate_seq | blob | raw |
-rwxr-xr-x | 2810 | transliterate_seq | blob | raw |
-rwxr-xr-x | 2982 | transliterate_vals | blob | raw |
-rwxr-xr-x | 2458 | trim_seq | blob | raw |
-rwxr-xr-x | 2603 | uchime_seq | blob | raw |
-rwxr-xr-x | 2982 | uclust_seq | blob | raw |
-rwxr-xr-x | 3046 | uniq_seq | blob | raw |
-rwxr-xr-x | 2836 | uniq_vals | blob | raw |
-rwxr-xr-x | 8804 | upload_to_ucsc | blob | raw |
-rwxr-xr-x | 1971 | uppercase_seq | blob | raw |
-rwxr-xr-x | 2501 | usearch_seq | blob | raw |
-rwxr-xr-x | 8104 | vmatch_seq | blob | raw |
-rwxr-xr-x | 3217 | write_2bit | blob | raw |
-rwxr-xr-x | 3575 | write_454 | blob | raw |
-rwxr-xr-x | 3283 | write_align | blob | raw |
-rwxr-xr-x | 3005 | write_bed | blob | raw |
-rwxr-xr-x | 4371 | write_blast | blob | raw |
-rwxr-xr-x | 2820 | write_fasta | blob | raw |
-rwxr-xr-x | 2517 | write_fasta_files | blob | raw |
-rwxr-xr-x | 2718 | write_fastq | blob | raw |
-rwxr-xr-x | 2537 | write_fastq_files | blob | raw |
-rwxr-xr-x | 3025 | write_fixedstep | blob | raw |
-rwxr-xr-x | 2805 | write_gff | blob | raw |
-rwxr-xr-x | 2638 | write_kiss | blob | raw |
-rwxr-xr-x | 10401 | write_mysql | blob | raw |
-rwxr-xr-x | 2753 | write_psl | blob | raw |
-rwxr-xr-x | 2910 | write_solid | blob | raw |
-rwxr-xr-x | 4803 | write_tab | blob | raw |
-rwxr-xr-x | 2480 | write_ucsc_config | blob | raw |