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file 1.axt 29710 -rw-r--r--
file 1.bam 3592 -rw-r--r--
file 1.bed 4202 -rw-r--r--
file 1.bed.spaces 4202 -rw-r--r--
file 1.bedgraph 566 -rw-r--r--
file 1.bigbed 154328 -rw-r--r--
file 1.bigwig 21218 -rw-r--r--
file 1.customtrack 265 -rw-r--r--
file 1.fasta 21625 -rw-r--r--
file 1.fastq 418 -rw-r--r--
file 1.fastqsanger 177 -rw-r--r--
file 1.fastqsolexa 418 -rw-r--r--
file 1.interval 234 -rw-r--r--
file 1.lav 2757 -rw-r--r--
file 1.pileup 21086 -rw-r--r--
file 1.sam 3444 -rw-r--r--
file 1.scf 139484 -rwxr-xr-x
file 1.sff 100 -rw-r--r--
file 1.tabular 99 -rw-r--r--
file 1.txt 208 -rw-r--r--
file 1.wig 273 -rw-r--r--
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file 1_bed_random_lines_1_seed_asdf_out.bed 65 -rw-r--r--
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file 2.fasta 671 -rw-r--r--
file 2.fastq 255 -rw-r--r--
file 2.fastqsanger 303 -rw-r--r--
file 2.fastqsolexa 181 -rw-r--r--
file 2.interval 501 -rw-r--r--
file 2.lav 376 -rw-r--r--
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file 2.txt 171 -rw-r--r--
file 2.wig 737 -rw-r--r--
file 2gen.fastq 181 -rw-r--r--
file 3.bed 4696 -rw-r--r--
file 3.bigwig 19082 -rw-r--r--
file 3.fasta 2673 -rw-r--r--
file 3.fastqsanger 1098 -rw-r--r--
file 3.maf 10929 -rw-r--r--
file 3.sam 1612 -rw-r--r--
file 3.wig 895 -rw-r--r--
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file 3unsorted.bam 1666 -rw-r--r--
file 4.bed 61 -rw-r--r--
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file 4.bed.gz 80 -rw-r--r--
file 4.bed.zip 198 -rw-r--r--
file 4.fasta 397 -rw-r--r--
file 4.maf 20031 -rw-r--r--
file 454.fasta 3024 -rw-r--r--
file 454.qual 6213 -rw-r--r--
file 454Score.pdf 10123 -rw-r--r--
file 454Score.png 4392 -rw-r--r--
file 454_high_quality_hist.pdf 6980 -rw-r--r--
file 5.bed 8754 -rw-r--r--
file 5.gff 1841 -rw-r--r--
file 5.gff3 8530 -rw-r--r--
file 5.maf 184750 -rw-r--r--
file 5_liftover_mapped.bed 8565 -rw-r--r--
file 5_liftover_unmapped.bed 253 -rw-r--r--
file 5_mult_liftover_mapped.bed 8630 -rw-r--r--
file 5_mult_liftover_unmapped.bed 162 -rw-r--r--
file 6.bed 650 -rw-r--r--
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file 8.bed 162 -rw-r--r--
file 9.bed 135 -rw-r--r--
file 9_hg18.bed 118 -rw-r--r--
file DNAseHSS.dat 74068 -rw-r--r--
file Extract_features1_out.gff 477 -rw-r--r--
file GRCm38mm10_chr5_34761740-34912521.fa 276538 -rw-r--r--
file Interval2Maf_pairwise_out.maf 8009 -rw-r--r--
file Ssuis.fasta 2040970 -rwxr-xr-x
file a.tab 818 -rw-r--r--
file a.txt 1335 -rw-r--r--
file add_scores_input1.interval 500 -rw-r--r--
file add_scores_input2.bed 486 -rw-r--r--
file add_scores_output1.interval 627 -rw-r--r--
file add_scores_output2.interval 620 -rw-r--r--
file aggregate_binned_scores_3.wig 13820 -rw-r--r--
file aggregate_binned_scores_in_intervals.out 894 -rw-r--r--
file aggregate_binned_scores_in_intervals2.interval 142 -rw-r--r--
file aggregate_binned_scores_in_intervals3.out 786 -rw-r--r--
file asian_chars_1.txt 80 -rw-r--r--
file axt_to_concat_fasta.dat 28317 -rw-r--r--
file axt_to_fasta.dat 29627 -rw-r--r--
file beam_output1.tab 94 -rw-r--r--
file beam_output2.tab 4514 -rw-r--r--
file bed2gff_out.gff 583 -rw-r--r--
file bfast_out1.sam 4409 -rw-r--r--
file bfast_out2.sam 7929 -rw-r--r--
file bfast_out3.sam 4346 -rw-r--r--
file blat_wrapper_test1.fa 4390 -rw-r--r--
file blat_wrapper_test1.out 9477 -rw-r--r--
file boxplot_summary_statistics_out.png 23237 -rw-r--r--
file build_ucsc_custom_track_out1.customtrack 721 -rw-r--r--
file cat_wrapper_out1.bed 8474 -rw-r--r--
file cca_out1.tabular 406 -rw-r--r--
file cca_out2.pdf 13558 -rw-r--r--
file cf-gene2exon.dat 12586 -rw-r--r--
file cf_maf2fasta_concat.dat 2206 -rw-r--r--
file cf_maf2fasta_new.dat 17258 -rw-r--r--
file cf_maf_limit_to_species.dat 8252 -rw-r--r--
file cf_maf_to_bed.dat 360 -rw-r--r--
file changeCase_out1.tabular 136 -rw-r--r--
file changeCase_out2.tabular 4202 -rw-r--r--
file chr_m.fasta 17000 -rw-r--r--
file codingSnps_input1.interval 819 -rw-r--r--
file codingSnps_input2.interval 556 -rw-r--r--
file codingSnps_inputGenes1.bed 3682 -rw-r--r--
file codingSnps_inputGenes2.bed 238263 -rw-r--r--
file codingSnps_output1.interval 1372 -rw-r--r--
file codingSnps_output2.interval 1156 -rw-r--r--
file codingSnps_output3.interval 1094 -rw-r--r--
file column_maker_out1.interval 4573 -rw-r--r--
file column_maker_out2.interval 257 -rw-r--r--
file column_maker_out3.interval 244 -rw-r--r--
file convert_SOLiD_color2nuc_test1.out 651 -rw-r--r--
file convert_SOLiD_color2nuc_test1.txt 661 -rw-r--r--
file cor.tabular 205 -rw-r--r--
file cor_out.txt 38 -rw-r--r--
file count_gff_features_out1.txt 2 -rw-r--r--
file count_gff_features_out2.txt 3 -rw-r--r--
file cuffcompare_in1.gtf 19854 -rw-r--r--
file cuffcompare_in1_liftover_mapped.bed 17073 -rw-r--r--
file cuffcompare_in1_liftover_unmapped.bed 3099 -rw-r--r--
file cuffcompare_in1_mult_liftover_mapped.bed 18270 -rw-r--r--
file cuffcompare_in1_mult_liftover_unmapped.bed 1740 -rw-r--r--
file cufflinks_out1.gtf 887 -rw-r--r--
file customTrack1.bed 623 -rw-r--r--
file dna_filter_in1.tabular 2993 -rw-r--r--
file dna_filter_out1.tabular 2138 -rw-r--r--
file dna_filter_out2.tabular 1909 -rw-r--r--
file dna_filter_out3.tabular 2570 -rw-r--r--
file dna_filter_out4.tabular 370 -rw-r--r--
file droPer1.bed 120 -rw-r--r--
file eq-addvalue.dat 4332 -rw-r--r--
file eq-condense.dat 4202 -rw-r--r--
file eq-convert.dat 4202 -rw-r--r--
file eq-createinterval.dat 29 -rw-r--r--
file eq-cut.dat 3942 -rw-r--r--
file eq-paste.dat 8477 -rw-r--r--
file eq-removebeginning.dat 3882 -rw-r--r--
file eq-showbeginning.dat 646 -rw-r--r--
file eq-showtail.dat 654 -rw-r--r--
file extract_genomic_dna_out1.fasta 20477 -rw-r--r--
file extract_genomic_dna_out2.fasta 272 -rw-r--r--
file extract_genomic_dna_out3.interval 22254 -rw-r--r--
file extract_genomic_dna_out4.gff 19505 -rw-r--r--
file extract_genomic_dna_out5.fasta 11122 -rw-r--r--
file extract_genomic_dna_out6.fasta 934 -rw-r--r--
file extract_genomic_dna_out7.fasta 842 -rw-r--r--
file fasta_to_tabular_out1.tabular 2990 -rw-r--r--
file fasta_to_tabular_out2.tabular 392 -rw-r--r--
file fasta_to_tabular_out3.tabular 1923 -rw-r--r--
file fasta_to_tabular_out4.tabular 2990 -rw-r--r--
file fasta_to_tabular_out5.tabular 2990 -rw-r--r--
file fasta_to_tabular_out6.tabular 2918 -rw-r--r--
file fasta_tool_compute_length_1.out 1396 -rw-r--r--
file fasta_tool_compute_length_2.out 2275 -rw-r--r--
file fasta_tool_compute_length_3.out 329 -rw-r--r--
file fastq_conv_in1.fastq 109 -rw-r--r--
file fastq_conv_out1.fastqsanger 110 -rw-r--r--
file fastq_conv_out2.fastqsolexa 178 -rw-r--r--
file fastq_conv_out4.fasta 104 -rw-r--r--
file fastq_gen_conv_in1.fastq 416 -rw-r--r--
file fastq_gen_conv_in2.fastq 443 -rw-r--r--
file fastq_gen_conv_out1.fastqsanger 312 -rw-r--r--
file fastq_gen_conv_out2.fastqsanger 369 -rw-r--r--
file fastq_stats_1_out.tabular 2525 -rw-r--r--
file fastqsolexa_to_fasta_qual_out2.fasta 84 -rw-r--r--
file fastqsolexa_to_fasta_qual_out4.fasta 146 -rw-r--r--
file filter1_in3.sam 13573 -rw-r--r--
file filter1_in5.tab 576 -rw-r--r--
file filter1_inbad.bed 310 -rw-r--r--
file filter1_test1.bed 260 -rw-r--r--
file filter1_test2.bed 317 -rw-r--r--
file filter1_test3.sam 815 -rw-r--r--
file filter1_test4.bed 286 -rw-r--r--
file filter1_test5.tab 494 -rw-r--r--
file filteredJoinedFlanksDNAse.dat 145 -rw-r--r--
file fr.csfasta 33973 -rw-r--r--
file fr.qualsolid 76446 -rw-r--r--
file fs-compare-2.dat 2581 -rw-r--r--
file fs-compare.dat 3172 -rw-r--r--
file fs-grep.dat 4202 -rw-r--r--
file fsa_interval2maf.dat 454311 -rw-r--r--
file gene_bed_maf_to_fasta_out.fasta 7480 -rw-r--r--
file gene_bed_maf_to_fasta_user_out.fasta 2994 -rw-r--r--
file gff2bed_in2.gff 2557 -rw-r--r--
file gff2bed_out.bed 1278 -rw-r--r--
file gff2bed_out2.bed 269 -rw-r--r--
file gff2bed_out3.bed 3736 -rw-r--r--
file gff_filter_attr_in1.gff 41686 -rw-r--r--
file gff_filter_by_attribute_out1.gff 9650 -rw-r--r--
file gff_filter_by_attribute_out2.gff 33501 -rw-r--r--
file gff_filter_by_feature_count_out1.gff 8741 -rw-r--r--
file gff_filter_by_feature_count_out2.gff 3824 -rw-r--r--
file gops_subtract_in1.gff 103056 -rw-r--r--
file gpass_and_beam_input.map 901 -rw-r--r--
file gpass_and_beam_input.ped 263000 -rw-r--r--
file gpass_output.txt 369 -rw-r--r--
file groupby_out1.dat 347 -rw-r--r--
file groupby_out2.dat 24 -rw-r--r--
file groupby_out3.tabular 2188 -rw-r--r--
file gsummary_out1.tabular 124 -rw-r--r--
file gtf2bedgraph_in.gtf 20868 -rw-r--r--
file gtf2bedgraph_out.bedgraph 3741 -rw-r--r--
file gtf_filter_by_attribute_values_list_in1.txt 33 -rw-r--r--
file gtf_filter_by_attribute_values_list_in2.gtf 16195 -rw-r--r--
file gtf_filter_by_attribute_values_list_in3.tabular 969 -rw-r--r--
file gtf_filter_by_attribute_values_list_out1.gtf 1872 -rw-r--r--
file gtf_filter_by_attribute_values_list_out2.gtf 7759 -rw-r--r--
file hg17chr22KnownGenes.dat 141024 -rw-r--r--
file histogram_in1.tabular 91 -rw-r--r--
file histogram_out1.pdf 8719 -rw-r--r--
file html_file.txt 3611 -rw-r--r--
file interval2maf_3from28way.maf 98881 -rw-r--r--
file interval_maf_to_merged_fasta_out.dat 94309 -rw-r--r--
file interval_maf_to_merged_fasta_out3.fasta 99782 -rw-r--r--
file interval_maf_to_merged_fasta_user_out.dat 94309 -rw-r--r--
file iris.tabular 4551 -rw-r--r--
file joiner_out1.bed 6256 -rw-r--r--
file joiner_out2.bed 7286 -rw-r--r--
file joiner_out3.bed 7479 -rw-r--r--
file joiner_out4.bed 7495 -rw-r--r--
file kcca_out1.tabular 19080 -rw-r--r--
file kcca_out2.tabular 10421 -rw-r--r--
file knownGeneUpstream500Flanks.dat 141024 -rw-r--r--
file kpca_out1.tabular 5783 -rw-r--r--
file kpca_out2.pdf 23896 -rw-r--r--
file lav_to_bed_out_1.bed 66 -rw-r--r--
file lav_to_bed_out_2.bed 68 -rw-r--r--
file ldInput1.txt 102436 -rw-r--r--
file ldOutput1.txt 233 -rw-r--r--
file lda_analy_output.txt 8821 -rw-r--r--
file linkToDavid.tabular 54 -rw-r--r--
file linkToDavid_1.out 266 -rw-r--r--
file linkToGProfile.tabular 75 -rw-r--r--
file linkToGProfile_1.out 430 -rw-r--r--
file lps_arrhythmia.tabular 367589 -rw-r--r--
file lps_arrhythmia_beta.tabular 6237 -rw-r--r--
file lps_arrhythmia_log.txt 8210 -rw-r--r--
file maf_by_block_number_out.dat 4639 -rw-r--r--
file maf_by_block_numbers.dat 8 -rw-r--r--
file maf_limit_size1_out.maf 10965 -rw-r--r--
file maf_reverse_complement_out.dat 10960 -rw-r--r--
file maf_split_by_species_collapsed_out.maf 4816 -rw-r--r--
file maf_split_by_species_in.maf 1131 -rw-r--r--
file maf_split_by_species_not_collapsed_out.maf 4852 -rw-r--r--
file maf_stats_interval_out.dat 32604 -rw-r--r--
file maf_stats_summary_out.dat 183 -rw-r--r--
file maf_thread_for_species.dat 4218 -rw-r--r--
file maf_to_interval_out_hg17.interval 2260 -rw-r--r--
file maf_to_interval_out_panTro1.interval 2263 -rw-r--r--
file master2snp_output.txt 923 -rw-r--r--
file masterVarTest.txt 390835 -rw-r--r--
file masterVar_output.txt 859 -rw-r--r--
file matrix_generator_for_pc_and_lda_input_1.tabular 17207 -rw-r--r--
file matrix_generator_for_pc_and_lda_input_2.tabular 1219 -rw-r--r--
file matrix_generator_for_pc_and_lda_output.tabular 18228 -rw-r--r--
file megablast_wrapper_test1.fa 869 -rw-r--r--
file megablast_wrapper_test1.out 1244 -rw-r--r--
file megablast_xml_parser_test1.gz 6728 -rw-r--r--
file megablast_xml_parser_test1_out.tabular 18613 -rw-r--r--
file mergeCols.dat 6926 -rw-r--r--
file mosaik_test_input.fastq 56274 -rw-r--r--
file mosaik_test_out.sam 70494 -rw-r--r--
file mosaik_test_ref.fasta 94497 -rw-r--r--
file mutation_data1.txt 11545 -rw-r--r--
file mutation_data1_interactive.svg 37924 -rw-r--r--
file mutation_data1_zoom3x.svg 31165 -rw-r--r--
file ngs_simulation_in1.fasta 2832 -rw-r--r--
file ngs_simulation_out1.png 12099 -rw-r--r--
file ngs_simulation_out2.tabular 763 -rw-r--r--
file ngs_simulation_out3.png 13857 -rw-r--r--
file pass_input.gff 4592 -rw-r--r--
file pass_output.tab 100 -rw-r--r--
file pca_out1.tabular 5197 -rw-r--r--
file pca_out2.pdf 14019 -rw-r--r--
file pca_out3.tabular 5244 -rw-r--r--
file pca_out4.pdf 14024 -rw-r--r--
file pca_out5.tabular 5201 -rw-r--r--
file pca_out6.pdf 13997 -rw-r--r--
file perm_in1.fastqsanger 2699 -rw-r--r--
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file perm_out3.fastqsanger 114 -rw-r--r--
file perm_out4.sam 11217 -rw-r--r--
file perm_out5.sam 2420 -rw-r--r--
file pgSnp2snp_output.txt 356333 -rw-r--r--
file pgSnpTest.ref.txt 463806 -rw-r--r--
file phiX.fasta 5473 -rw-r--r--
file plot_for_lda_output.pdf 9823 -rw-r--r--
file qualscores.qual454 5691 -rw-r--r--
file qualscores.qualsolid 2565 -rw-r--r--
file qualsolid.stats 1657 -rw-r--r--
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file rgenetics.fam 603 -rw-r--r--
file rgenetics.map 600 -rw-r--r--
file rgenetics.ped 4603 -rw-r--r--
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file rmap_wrapper_test1.fasta 431 -rw-r--r--
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file rmapq_wrapper_test1.qual 7200 -rw-r--r--
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file rr.qualsolid 77810 -rw-r--r--
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file s2fq_paired_F3.csfasta 2530 -rw-r--r--
file s2fq_paired_F3_QV.qualsolid 4007 -rw-r--r--
file s2fq_paired_R3.csfasta 2530 -rw-r--r--
file s2fq_paired_R3_QV.qualsolid 4019 -rw-r--r--
file s2fq_phiX.csfasta 7838 -rw-r--r--
file s2fq_phiX.qualsolid 16646 -rw-r--r--
file scatterplot_in1.tabular 91 -rw-r--r--
file scatterplot_out1.pdf 3152 -rw-r--r--
file secure_hash_message_digest_out1.tabular 388 -rw-r--r--
file sff_converter_fasta.dat 1730 -rw-r--r--
file sff_converter_fastq.dat 3418 -rw-r--r--
file sff_converter_qual.dat 5079 -rw-r--r--
file sff_converter_xml_1.dat 566 -rw-r--r--
file sff_converter_xml_2.dat 566 -rw-r--r--
file short_reads_trim_seq_out1.fasta 2096 -rw-r--r--
file short_reads_trim_seq_out2.fasta 981 -rw-r--r--
file shrimp_cs_test1.csfasta 166534 -rw-r--r--
file shrimp_cs_test1.out 142793 -rw-r--r--
file shrimp_phix_anc.fa 5398 -rwxr-xr-x
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file shrimp_wrapper_test1.out1 538 -rw-r--r--
file sift_variants.tab 600 -rw-r--r--
file sift_variants_result.tab 2982 -rw-r--r--
file simple_line.txt 24 -rw-r--r--
file simple_line_alternative.txt 33 -rw-r--r--
file simple_line_x2.txt 48 -rw-r--r--
file simple_line_x3.txt 72 -rw-r--r--
file simple_line_x5.txt 120 -rw-r--r--
file simple_lines_both.txt 57 -rw-r--r--
file simple_lines_interleaved.txt 115 -rw-r--r--
file snpFreqInput.txt 299 -rw-r--r--
file snpFreqTestOut.txt 880 -rw-r--r--
file solexa.fasta 1220 -rw-r--r--
file solexa.qual 21600 -rw-r--r--
file solexa.tabular 1530 -rw-r--r--
file solexaScore.png 5415 -rw-r--r--
file solexa_high_quality_hist.pdf 4080 -rw-r--r--
file solid2fastq_out_1.fastq 59975 -rw-r--r--
file solid2fastq_out_2.fastq 59236 -rw-r--r--
file solid2fastq_out_3.fastq 59236 -rw-r--r--
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file tabular_to_fasta_out1.fasta 1560 -rw-r--r--
file tinywga.bed 253 -rw-r--r--
file tinywga.bim 700 -rw-r--r--
file tinywga.fam 603 -rw-r--r--
file tinywga.map 600 -rw-r--r--
file tinywga.ped 4603 -rw-r--r--
file tinywga.ped.space_to_tab 4603 -rw-r--r--
file tophat_in1.fasta 680 -rw-r--r--
file trimmer_a_f_c0_s1_e13_i62.dat 73 -rw-r--r--
file trimmer_a_f_c2_s1_e2_i62.dat 71 -rw-r--r--
file trimmer_a_f_c2_s2_e-2_i62.dat 70 -rw-r--r--
file trimmer_tab_delimited.dat 82 -rw-r--r--
file uniq_out.dat 151 -rw-r--r--
file vcf2pgSnp_input.vcf 8684 -rw-r--r--
file vcf2pgSnp_output.pgSnp 637 -rw-r--r--
file velvet_test_reads.fa 8888944 -rw-r--r--
file wc_gnu_out_1.tabular 36 -rw-r--r--
file wc_gnu_out_2.tabular 12 -rw-r--r--