Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.5 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.3 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.2.1 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.1.1.1 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.1.2 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.1.1 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1 |
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.0 |
pygenomeTracks |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
pygenometracks | 3.5 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
tracks_8|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_3|track_file_style_conditional|title: TAD state tracks_16|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_16|track_file_style_conditional|title: bed6 global max row tracks_9|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_9|track_file_style_conditional|height_bigwig: 4 tracks_4|track_file_style_conditional|type|type_selector: matrix tracks_4|track_file_style_conditional|title: TAD separation score (Ramirez et al.) tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option tracks_5|track_file_style_conditional|spacer_height: 1 image_file_format: png tracks_3|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_7|track_file_style_conditional|color: blue tracks_14|track_file_style_conditional|bed_style|bed_advanced|gene_rows: 3 tracks_2|track_file_style_conditional|track_file_style_selector: spacer_option tracks_9|track_file_style_conditional|title: rep 1 test lw=0.2 tracks_12|track_file_style_conditional|title: genes tracks_6|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_17|track_file_style_conditional|track_input_bed_single: domains.bed tracks_12|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_1|track_file_style_conditional|boundaries_file: domains.bed tracks_11|track_file_style_conditional|spacer_height: 0.5 tracks_0|track_file_style_conditional|xaxis_where: top tracks_6|track_file_style_conditional|height_bedgraph: 4 tracks_11|track_file_style_conditional|track_file_style_selector: spacer_option tracks_16|track_file_style_conditional|height_bed: 20 tracks_4|track_file_style_conditional|height_bedgraph: 10 tracks_1|track_file_style_conditional|depth: 200000 tracks_3|track_file_style_conditional|height_chrom: 0.5 tracks_14|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_10|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_14|track_file_style_conditional|title: max num rows 3 tracks_7|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_16|track_file_style_conditional|track_input_bed: dm3_genes.bed6.gz tracks_10|track_file_style_conditional|color: black tracks_3|track_file_style_conditional|track_input_bed: tad_classification.bed tracks_3|track_file_style_conditional|labels: False tracks_10|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_8|track_file_style_conditional|type_conditional|width_line: 1 tracks_8|track_file_style_conditional|title: rep 1 test line tracks_17|track_file_style_conditional|track_file_style_selector: vlines_track_option tracks_16|track_file_style_conditional|fontsize: 10 tracks_7|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_12|track_file_style_conditional|fontsize: 10 tracks_9|track_file_style_conditional|type_conditional|width_line: 0.1 tracks_10|track_file_style_conditional|height_bigwig: 4 tracks_7|track_file_style_conditional|title: rep 1 test fill tracks_1|track_file_style_conditional|transform: log1p tracks_8|track_file_style_conditional|type_conditional|type_selector: line_option tracks_8|track_file_style_conditional|color: red tracks_15|track_file_style_conditional|track_file_style_selector: spacer_option tracks_9|track_file_style_conditional|color: red tracks_3|track_file_style_conditional|track_file_style_selector: chrom_states_option tracks_7|track_file_style_conditional|height_bigwig: 4 tracks_14|track_file_style_conditional|fontsize: 8 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|spacer_height: 0.05 tracks_6|track_file_style_conditional|color: blue tracks_6|track_file_style_conditional|title: bedgraph tracks_8|track_file_style_conditional|height_bigwig: 4 tracks_5|track_file_style_conditional|track_file_style_selector: spacer_option tracks_7|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_13|track_file_style_conditional|track_file_style_selector: spacer_option tracks_12|track_file_style_conditional|height_bed: 5 tracks_10|track_file_style_conditional|type_conditional|width_point: 0.5 tracks_10|track_file_style_conditional|title: rep 1 test point:0.5 tracks_4|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz tracks_8|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_14|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_16|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_10|track_file_style_conditional|type_conditional|type_selector: point_option tracks_15|track_file_style_conditional|spacer_height: 1 tracks_9|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_13|track_file_style_conditional|spacer_height: 1 tracks_9|track_file_style_conditional|type_conditional|type_selector: line_option tracks_12|track_file_style_conditional|track_file_style_selector: gene_track_option region: chrX:3000000-3500000 tracks_14|track_file_style_conditional|height_bed: 3 |
attributes: name |
Li_et_al_2015.h5 domains.bed tad_classification.bed tad_score.gz bedgraph_chrx_2e6_5e6.bg bigwig_chrx_2e6_5e6.bw dm3_genes.bed.gz dm3_genes.bed6.gz domains.bed name |
Test-2 |
tracks_2|track_file_style_conditional|show_data: True tracks_2|track_file_style_conditional|height_bigwig: 4 tracks_3|track_file_style_conditional|y_values: 50 tracks_4|track_file_style_conditional|title: hlines tracks_4|track_file_style_conditional|track_file_style_selector: hlines_track_option image_file_format: png tracks_2|track_file_style_conditional|title: nans_to_zeros tracks_2|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_4|track_file_style_conditional|color: purple tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_1|track_file_style_conditional|title: rep 1 test line tracks_3|track_file_style_conditional|overlay_select: share-y tracks_3|track_file_style_conditional|color: orange tracks_2|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|height_bigwig: 4 tracks_1|track_file_style_conditional|type_conditional|type_selector: line_option tracks_4|track_file_style_conditional|invert_orientation: True tracks_2|track_file_style_conditional|color: blue tracks_3|track_file_style_conditional|title: tracks_4|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|line_style: dashed tracks_2|track_file_style_conditional|type_conditional|type_selector: line_option tracks_1|track_file_style_conditional|type_conditional|width_line: 1 tracks_2|track_file_style_conditional|type_conditional|width_line: 1 tracks_1|track_file_style_conditional|track_input_bigwig: ['bigwig_chrx_2e6_5e6.bw', 'bigwig_chrx_2e6_5e6.bw'] tracks_3|track_file_style_conditional|line_width: 2 tracks_4|track_file_style_conditional|min_value: 12 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|color: red tracks_2|track_file_style_conditional|reading_bw_conditional|nans_to_zeros: True tracks_3|track_file_style_conditional|track_file_style_selector: hlines_track_option region: chrX:3000000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_4|track_file_style_conditional|y_values: 0, 10, 20, 100 |
attributes: name |
bigwig_chrx_2e6_5e6.bw bigwig_chrx_2e6_5e6.bw name |
Test-3 |
tracks_5|track_file_style_conditional|height_bedgraph: 4 tracks_11|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_12|track_file_style_conditional|color_bed|color: RdYlBu_r tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|colormap: RdYlBu_r tracks_1|track_file_style_conditional|boundaries_file: domains.bed tracks_6|track_file_style_conditional|height_bedgraph: 4 tracks_9|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_14|track_file_style_conditional|track_input_bed: domains.bed tracks_10|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_9|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_10|track_file_style_conditional|color: black tracks_8|track_file_style_conditional|type_conditional|width_point: 5 tracks_3|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_13|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_1|track_file_style_conditional|transform: log1p tracks_5|track_file_style_conditional|title: bedgraph with negative values tracks_2|track_file_style_conditional|track_input_bed: tad_classification.bed tracks_14|track_file_style_conditional|fontsize: 10 tracks_3|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_12|track_file_style_conditional|height_bed: 20 tracks_13|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_9|track_file_style_conditional|reading_bw_conditional|summary_method: min tracks_10|track_file_style_conditional|reading_bw_conditional|summary_method: min tracks_8|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_2|track_file_style_conditional|height_chrom: 0.5 tracks_6|track_file_style_conditional|color: blue tracks_3|track_file_style_conditional|invert_orientation: True tracks_14|track_file_style_conditional|height_bed: 2 tracks_8|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_15|track_file_style_conditional|labels|plot_labels: false tracks_3|track_file_style_conditional|transform: no tracks_4|track_file_style_conditional|track_file_style_selector: spacer_option image_file_format: png tracks_7|track_file_style_conditional|color: blue tracks_11|track_file_style_conditional|height_bed: 5 tracks_2|track_file_style_conditional|track_file_style_selector: chrom_states_option tracks_12|track_file_style_conditional|title: bed6 global max row color from score tracks_14|track_file_style_conditional|display: interleaved tracks_7|track_file_style_conditional|title: rep 1 test fill tracks_11|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_10|track_file_style_conditional|overlay_select: share-y tracks_10|track_file_style_conditional|height_bigwig: 10 tracks_14|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=bed_rgb tracks_15|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_2|track_file_style_conditional|labels: False tracks_3|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) inverted no transform tracks_7|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_12|track_file_style_conditional|fontsize: 10 tracks_6|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_9|track_file_style_conditional|color: #c00000 tracks_14|track_file_style_conditional|labels|plot_labels: false tracks_10|track_file_style_conditional|type_conditional|type_selector: line_option tracks_13|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=red tracks_14|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_5|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_3|track_file_style_conditional|depth: 200000 tracks_2|track_file_style_conditional|title: TAD state tracks_13|track_file_style_conditional|fontsize: 10 tracks_1|track_file_style_conditional|depth: 200000 tracks_8|track_file_style_conditional|reading_bw_conditional|number_of_bins: 100 tracks_8|track_file_style_conditional|color: red tracks_10|track_file_style_conditional|spacer_height: 1 tracks_10|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_13|track_file_style_conditional|track_input_bed: domains.bed tracks_8|track_file_style_conditional|height_bigwig: 10 tracks_8|track_file_style_conditional|title: (red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value) tracks_8|track_file_style_conditional|reading_bw_conditional|summary_method: max tracks_14|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_15|track_file_style_conditional|track_input_bed: domains.bed tracks_4|track_file_style_conditional|spacer_height: 1 tracks_7|track_file_style_conditional|height_bigwig: 4 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_13|track_file_style_conditional|height_bed: 2 tracks_11|track_file_style_conditional|title: genes in ucsc tracks_6|track_file_style_conditional|title: bedgraph tracks_13|track_file_style_conditional|display: interleaved tracks_5|track_file_style_conditional|color_negative|color: red tracks_12|track_file_style_conditional|color_bed|color_bed_select: colormap tracks_10|track_file_style_conditional|reading_bw_conditional|number_of_bins: 30000 tracks_5|track_file_style_conditional|color: black region: chrX:3000000-3500000 tracks_3|track_file_style_conditional|colormap: Reds tracks_15|track_file_style_conditional|height_bed: 2 tracks_15|track_file_style_conditional|display: interleaved tracks_9|track_file_style_conditional|height_bigwig: 10 tracks_3|track_file_style_conditional|min_value: 5 tracks_13|track_file_style_conditional|border_color_bed|color: red tracks_5|track_file_style_conditional|track_input_bedgraph: test_with_neg_values.bg.gz tracks_6|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_12|track_file_style_conditional|track_input_bed: dm3_genes.bed6.gz tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_9|track_file_style_conditional|overlay_select: share-y tracks_15|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=none tracks_13|track_file_style_conditional|border_color_bed|border_color_bed_select: manually tracks_15|track_file_style_conditional|border_color_bed|border_color_bed_select: none tracks_7|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_15|track_file_style_conditional|fontsize: 10 tracks_5|track_file_style_conditional|color_negative|color_negative_select: true tracks_3|track_file_style_conditional|max_value: 70 tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) log1p tracks_11|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_12|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_15|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_13|track_file_style_conditional|labels|plot_labels: false tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_7|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_14|track_file_style_conditional|border_color_bed|border_color_bed_select: bed_rgb tracks_11|track_file_style_conditional|fontsize: 10 tracks_0|track_file_style_conditional|xaxis_where: top tracks_8|track_file_style_conditional|type_conditional|type_selector: point_option tracks_9|track_file_style_conditional|type_conditional|type_selector: line_option tracks_12|track_file_style_conditional|track_file_style_selector: gene_track_option |
attributes: name |
Li_et_al_2015.h5 domains.bed tad_classification.bed test_with_neg_values.bg.gz bedgraph_chrx_2e6_5e6.bg bigwig_chrx_2e6_5e6.bw dm3_genes.bed.gz dm3_genes.bed6.gz domains.bed name |
Test-4 |
tracks_0|track_file_style_conditional|color: #00b0f0 tracks_0|track_file_style_conditional|height_bigwig: 7 tracks_0|track_file_style_conditional|title: (bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins) tracks_0|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|overlay_select: share-y region: X:2700000-3100000 image_file_format: png tracks_1|track_file_style_conditional|title: tracks_1|track_file_style_conditional|reading_bw_conditional|number_of_bins: 300 tracks_0|track_file_style_conditional|reading_bw_conditional|number_of_bins: 2000 tracks_2|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_0|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_2|track_file_style_conditional|xaxis_where: bottom tracks_1|track_file_style_conditional|color: #ff0000 tracks_1|track_file_style_conditional|alpha: 0.5 tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option |
attributes: name |
bigwig_chrx_2e6_5e6.bw name |
Test-5 |
tracks_1|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_1|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_1|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|height_bed: 10 region: X:3000000-3300000 tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png tracks_1|track_file_style_conditional|title: test tracks_2|track_file_style_conditional|title: test tracks_0|track_file_style_conditional|xaxis_where: top tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78_asbed4.bed.gz |
attributes: name |
dm3_subset_BDGP5.78.gtf.gz dm3_subset_BDGP5.78_asbed4.bed.gz name |
Test-6 |
tracks_2|track_file_style_conditional|display|max_value: 50 tracks_0|track_file_style_conditional|title: box tracks_2|track_file_style_conditional|display|use_summit: True tracks_3|track_file_style_conditional|height_narrow_peak: 4 tracks_0|track_file_style_conditional|height_narrow_peak: 4 tracks_4|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png tracks_1|track_file_style_conditional|display|use_summit: True tracks_2|track_file_style_conditional|title: peak width 3 tracks_3|track_file_style_conditional|display|use_summit: False tracks_2|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_3|track_file_style_conditional|display|display_selector: peak tracks_1|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_2|track_file_style_conditional|show_labels: False tracks_4|track_file_style_conditional|xaxis_where: bottom tracks_1|track_file_style_conditional|display|display_selector: box tracks_3|track_file_style_conditional|color: #000000 tracks_1|track_file_style_conditional|show_labels: True tracks_1|track_file_style_conditional|line_width: 2 tracks_3|track_file_style_conditional|display|show_data: False tracks_3|track_file_style_conditional|title: peak no data range tracks_0|track_file_style_conditional|color: #9bbb59 tracks_2|track_file_style_conditional|display|show_data: True tracks_3|track_file_style_conditional|show_labels: True tracks_2|track_file_style_conditional|height_narrow_peak: 4 tracks_1|track_file_style_conditional|height_narrow_peak: 4 tracks_2|track_file_style_conditional|spacer_height: 0.5 tracks_0|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_1|track_file_style_conditional|color: #9bbb59 tracks_2|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_0|track_file_style_conditional|show_labels: True tracks_3|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_3|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_0|track_file_style_conditional|display|display_selector: box region: X:2760000-2802000 tracks_0|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_1|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_1|track_file_style_conditional|title: box line_width = 2 tracks_2|track_file_style_conditional|color: #c0504d tracks_2|track_file_style_conditional|display|display_selector: peak tracks_0|track_file_style_conditional|display|use_summit: True tracks_2|track_file_style_conditional|display|width_adjust: 3 |
attributes: name |
test2.narrowPeak name |
Test-7 |
tracks_2|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: manually tracks_6|track_file_style_conditional|labels|all_labels_inside: True tracks_2|track_file_style_conditional|bed_style|bed_advanced|gtf|merge_transcripts: True tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png tracks_2|track_file_style_conditional|title: gtf tracks_3|track_file_style_conditional|color_bed|color_bed_select: colormap tracks_6|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_4|track_file_style_conditional|title: genes with utr as bed_rgb tracks_6|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_1|track_file_style_conditional|title: genes tracks_6|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_5|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_2|track_file_style_conditional|bed_style|bed_advanced|color_utr|color: #ff0000 tracks_6|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: like tracks_6|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_1|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|height_bed: 10 tracks_5|track_file_style_conditional|labels|plot_labels: true tracks_5|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_5|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_5|track_file_style_conditional|labels|labels_in_margin: True tracks_5|track_file_style_conditional|title: genes with coding as bed_rgb - labels_in_margin tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|bed_style|bed_advanced|gtf|prefered_name: gene_name tracks_5|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|height_bed: 10 tracks_4|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_6|track_file_style_conditional|title: genes bed_rgb like - all_labels_inside tracks_4|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: bed_rgb tracks_2|track_file_style_conditional|bed_style|bed_advanced|height_utr: 0.75 region: chrX:3300000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_3|track_file_style_conditional|color_bed|color: cool_r tracks_4|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_3|track_file_style_conditional|title: genes with scores tracks_6|track_file_style_conditional|labels|plot_labels: true |
attributes: name |
dm3_genes.bed.gz dm3_subset_BDGP5.78.gtf.gz dm3_genes_withrgbandscore.bed.gz name |
Test-8 |
tracks_1|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|bed_style|bed_advanced|max_labels: 15 tracks_2|track_file_style_conditional|bed_style|bed_advanced|line_width: 2 region: chrX:3300000-3500000 tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_1|track_file_style_conditional|bed_style|bed_style_select: UCSC image_file_format: png tracks_1|track_file_style_conditional|title: dm3_genes.bed tracks_2|track_file_style_conditional|title: genes.bed.gz tracks_0|track_file_style_conditional|xaxis_where: top tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|bed_style|bed_advanced|arrow_interval: 10 tracks_1|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz |
attributes: name |
dm3_genes.bed.gz name |
Test-9 |
tracks_2|track_file_style_conditional|color_bed|color_bed_select: manually tracks_4|track_file_style_conditional|track_file_style_selector: vlines_track_option image_file_format: png tracks_2|track_file_style_conditional|title: test tracks_3|track_file_style_conditional|color_bed|color_bed_select: manually tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_1|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_0|track_file_style_conditional|xaxis_where: top tracks_3|track_file_style_conditional|bed_style|arrowhead_included: True tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_3|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_1|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|spacer_height: 1 tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78_asbed4.bed.gz tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_3|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|track_input_bed_single: dm3_subset_BDGP5.78_asbed4.bed.gz region: X:3133000-3138000 tracks_1|track_file_style_conditional|title: test tracks_3|track_file_style_conditional|color_bed|color: red tracks_3|track_file_style_conditional|title: test tracks_2|track_file_style_conditional|color_bed|color: red |
attributes: name |
dm3_subset_BDGP5.78.gtf.gz dm3_subset_BDGP5.78_asbed4.bed.gz name |
Test-10 |
tracks_1|track_file_style_conditional|color_bed|color_bed_select: manually tracks_3|track_file_style_conditional|use_middle: True tracks_1|track_file_style_conditional|spacer_height: 1 image_file_format: png tracks_2|track_file_style_conditional|title: bedgraph tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|type_conditional|type_selector: line_option tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_3|track_file_style_conditional|height_bedgraph: 4 tracks_1|track_file_style_conditional|color_bed|color: yellow tracks_3|track_file_style_conditional|color: blue tracks_2|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_3|track_file_style_conditional|title: bedgraph tracks_1|track_file_style_conditional|track_input_bed: domains.bed tracks_2|track_file_style_conditional|type_conditional|type_selector: line_option tracks_3|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_2|track_file_style_conditional|height_bedgraph: 4 tracks_1|track_file_style_conditional|display: triangles tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|height_bed: 6 tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option region: X:3340000-3380000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_2|track_file_style_conditional|color: blue |
attributes: name |
domains.bed bedgraph_chrx_2e6_5e6.bg name |
Test-11 |
tracks_4|track_file_style_conditional|type|type_selector: lines tracks_2|track_file_style_conditional|track_file_style_selector: spacer_option tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option image_file_format: png tracks_1|track_file_style_conditional|scale_factor: 2.0 tracks_3|track_file_style_conditional|type|pos_score_in_bin: block tracks_3|track_file_style_conditional|type|type_selector: lines tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_4|track_file_style_conditional|height_bedgraph: 10 tracks_1|track_file_style_conditional|depth: 100000 tracks_3|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_3|track_file_style_conditional|title: TAD separation score (Ramirez et al.) tracks_3|track_file_style_conditional|height_bedgraph: 10 tracks_1|track_file_style_conditional|transform: log1p tracks_2|track_file_style_conditional|spacer_height: 0.05 tracks_4|track_file_style_conditional|type|pos_score_in_bin: center tracks_1|track_file_style_conditional|show_masked_bins: True tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_3|track_file_style_conditional|type|show_data: True tracks_4|track_file_style_conditional|type|plot_horizontal_lines: False tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option tracks_4|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz region: chrX:3250000-3400000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_4|track_file_style_conditional|title: TAD separation score (Ramirez et al.) tracks_3|track_file_style_conditional|type|plot_horizontal_lines: True |
attributes: name |
Li_et_al_2015.h5 tad_score.gz name |
Test-12 |
tracks_3|track_file_style_conditional|color_link|color_link_select: colormap image_file_format: png tracks_2|track_file_style_conditional|title: tracks_2|track_file_style_conditional|track_file_style_selector: link_track_option tracks_1|track_file_style_conditional|colormap: Purples tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_2|track_file_style_conditional|color_link|color: red tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_3|track_file_style_conditional|track_input_link: test.arcs tracks_2|track_file_style_conditional|overlay_select: share-y tracks_1|track_file_style_conditional|depth: 190000 tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_2|track_file_style_conditional|color_link|color_link_select: manually tracks_3|track_file_style_conditional|title: tracks_3|track_file_style_conditional|max_value: 5 tracks_1|track_file_style_conditional|transform: no tracks_3|track_file_style_conditional|height: 5 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|links_type: loops tracks_3|track_file_style_conditional|color_link|color: hot tracks_2|track_file_style_conditional|line_width: 10 tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option tracks_2|track_file_style_conditional|track_input_link: test.arcs region: chrX:3000000-3300000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_3|track_file_style_conditional|invert_orientation: True |
attributes: name |
Li_et_al_2015.h5 test.arcs name |
Test-13 |
tracks_0|track_file_style_conditional|title: default tracks_1|track_file_style_conditional|color_link|color: #000000 tracks_0|track_file_style_conditional|track_input_link: test.arcs tracks_3|track_file_style_conditional|color_link|color_link_select: manually tracks_3|track_file_style_conditional|compact_arcs_level: 2 tracks_2|track_file_style_conditional|title: compacted tracks_2|track_file_style_conditional|track_file_style_selector: link_track_option tracks_0|track_file_style_conditional|color_link|color: #000000 tracks_1|track_file_style_conditional|color_link|color_link_select: manually tracks_1|track_file_style_conditional|track_file_style_selector: link_track_option tracks_2|track_file_style_conditional|color_link|color: #000000 tracks_3|track_file_style_conditional|track_input_link: test.arcs tracks_2|track_file_style_conditional|color_link|color_link_select: manually tracks_1|track_file_style_conditional|ylim: 20000 tracks_3|track_file_style_conditional|title: highly compacted tracks_2|track_file_style_conditional|compact_arcs_level: 1 tracks_0|track_file_style_conditional|track_file_style_selector: link_track_option image_file_format: png tracks_3|track_file_style_conditional|color_link|color: #000000 tracks_0|track_file_style_conditional|color_link|color_link_select: manually tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option tracks_2|track_file_style_conditional|track_input_link: test.arcs region: chrX:3000000-3300000 tracks_1|track_file_style_conditional|title: ylim 20kb tracks_1|track_file_style_conditional|track_input_link: test.arcs |
attributes: name |
test.arcs name |
Test-14 |
tracks_1|track_file_style_conditional|title: default tracks_2|track_file_style_conditional|line_width: 2 tracks_0|track_file_style_conditional|spacer_height: 1.0 tracks_2|track_file_style_conditional|size: 100002 tracks_2|track_file_style_conditional|fontsize: 8 tracks_2|track_file_style_conditional|spacer_height: 4 image_file_format: png global_args|trackLabelFraction: 0.5 tracks_2|track_file_style_conditional|title: scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5 tracks_2|track_file_style_conditional|sb_where: right tracks_2|track_file_style_conditional|color: red tracks_2|track_file_style_conditional|track_file_style_selector: scale_bar_option global_args|title: Scale bar tracks_0|track_file_style_conditional|track_file_style_selector: spacer_option tracks_2|track_file_style_conditional|x_center: 3200000 global_args|trackLabelHAlign: center tracks_1|track_file_style_conditional|spacer_height: 1 region: chrX:3000000-3300000 tracks_1|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_2|track_file_style_conditional|alpha: 0.5 |
attributes: name |
name |
Test-15 |
tracks_4|track_file_style_conditional|title: tssarrow 5kb tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png tracks_2|track_file_style_conditional|title: UCSC tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|bed_style|bed_advanced|arrow_length: 5000 tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_0|track_file_style_conditional|xaxis_where: bottom tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_4|track_file_style_conditional|bed_style|bed_style_select: tssarrow tracks_3|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_1|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_2|track_file_style_conditional|bed_style|bed_advanced|arrow_interval: 10 tracks_1|track_file_style_conditional|height_bed: 10 tracks_4|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option region: chrX:3300000-3500000 tracks_1|track_file_style_conditional|title: flybase tracks_3|track_file_style_conditional|bed_style|bed_style_select: tssarrow tracks_4|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_3|track_file_style_conditional|title: tssarrow |
attributes: name |
dm3_genes.bed.gz name |
Test-16 |
tracks_0|track_file_style_conditional|color: #00b0f0 tracks_0|track_file_style_conditional|height_bigwig: 7 tracks_0|track_file_style_conditional|title: (bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins) tracks_0|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|overlay_select: share-y region: X:2700000-3100000 global_args|decreasingXAxis: True image_file_format: png tracks_1|track_file_style_conditional|title: tracks_1|track_file_style_conditional|reading_bw_conditional|number_of_bins: 300 tracks_0|track_file_style_conditional|reading_bw_conditional|number_of_bins: 2000 tracks_2|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_0|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_2|track_file_style_conditional|xaxis_where: bottom tracks_1|track_file_style_conditional|color: #ff0000 tracks_1|track_file_style_conditional|alpha: 0.5 tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option |
attributes: name |
bigwig_chrx_2e6_5e6.bw name |
Test-17 |
tracks_2|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|title: bedgraph color = blue transform = no tracks_8|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_3|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_4|track_file_style_conditional|op|operation: log(2+file) tracks_4|track_file_style_conditional|title: bedgraph color = green operation = log(2+file) min_value = 0.7 tracks_5|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|min_value: 0 image_file_format: png tracks_2|track_file_style_conditional|title: bedgraph color = red transform = log min_value = 1 tracks_5|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|color: black tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_4|track_file_style_conditional|color: green tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|min_value: 0 tracks_6|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|y_axis_values: True tracks_2|track_file_style_conditional|min_value: 1 tracks_3|track_file_style_conditional|logScale_conditional|log_pseudocount: 2 tracks_3|track_file_style_conditional|color: green tracks_2|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_4|track_file_style_conditional|height_bedgraph: 5 tracks_3|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_6|track_file_style_conditional|op|operation: log2(1+file) tracks_0|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|show_data: True tracks_7|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_2|track_file_style_conditional|color: red tracks_4|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|color: blue tracks_7|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_1|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_2|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original tracks_2|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|min_value: 0 tracks_3|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|min_value: 0.7 tracks_0|track_file_style_conditional|height_bedgraph: 5 tracks_0|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_5|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_7|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_1|track_file_style_conditional|show_data: True tracks_6|track_file_style_conditional|title: bedgraph color = black operation = log2(1+file) min_value = 0 region: chr2:73,800,000-75,744,000 tracks_1|track_file_style_conditional|title: bedgraph color = blue transform = log tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|title: bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 tracks_5|track_file_style_conditional|color: black tracks_8|track_file_style_conditional|xaxis_where: bottom tracks_6|track_file_style_conditional|min_value: 0 tracks_6|track_file_style_conditional|color: black tracks_0|track_file_style_conditional|show_data: True |
attributes: name |
GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz name |
Test-18 |
tracks_2|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|op|operation: log1p(file) tracks_4|track_file_style_conditional|color_negative|color_negative_select: true tracks_4|track_file_style_conditional|op|operation: file - second_file tracks_4|track_file_style_conditional|title: operation = file - second_file tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option image_file_format: png tracks_2|track_file_style_conditional|title: second_file summary_method = mean tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_4|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|height_bedgraph: 4 tracks_0|track_file_style_conditional|xaxis_where: top tracks_2|track_file_style_conditional|min_value: 0 tracks_3|track_file_style_conditional|color: blue tracks_4|track_file_style_conditional|height_bedgraph: 8 tracks_3|track_file_style_conditional|spacer_height: 0.5 tracks_2|track_file_style_conditional|track_input_bedgraph: bedgraph2_X_2.5e6_3.5e6.bdg tracks_2|track_file_style_conditional|color: red tracks_3|track_file_style_conditional|title: operation = log1p(file) (no summary_method) tracks_4|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|height_bedgraph: 4 tracks_4|track_file_style_conditional|color_negative|color: red tracks_3|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_1|track_file_style_conditional|reading_bdg_as_bw|summary_method: mean tracks_2|track_file_style_conditional|height_bedgraph: 4 tracks_2|track_file_style_conditional|spacer_height: 0.5 tracks_3|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_4|track_file_style_conditional|max_value: 30 tracks_4|track_file_style_conditional|min_value: -30 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|reading_bdg_as_bw|number_of_bins: 20 tracks_1|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_1|track_file_style_conditional|show_data: True region: chrX:2700000-3100000 tracks_4|track_file_style_conditional|op|second_file: bedgraph2_X_2.5e6_3.5e6.bdg tracks_1|track_file_style_conditional|title: file summary_method = mean number_of_bins=20 tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|min_value: 0 tracks_1|track_file_style_conditional|max_value: 30 tracks_2|track_file_style_conditional|max_value: 30 tracks_2|track_file_style_conditional|reading_bdg_as_bw|summary_method: mean |
attributes: name |
bedgraph_chrx_2e6_5e6.bg bedgraph2_X_2.5e6_3.5e6.bdg name |
Test-19 |
tracks_2|track_file_style_conditional|show_data: True tracks_2|track_file_style_conditional|grid: True tracks_0|track_file_style_conditional|title: bedgraph color = blue transform = no tracks_5|track_file_style_conditional|grid: True tracks_8|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_3|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_4|track_file_style_conditional|op|operation: log(2+file) tracks_4|track_file_style_conditional|title: bedgraph color = green operation = log(2+file) min_value = 0.7 tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|min_value: 0 image_file_format: png tracks_2|track_file_style_conditional|title: bedgraph color = red transform = log min_value = 1 tracks_3|track_file_style_conditional|grid: True tracks_4|track_file_style_conditional|grid: True tracks_7|track_file_style_conditional|color: black tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_4|track_file_style_conditional|color: green tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|min_value: 0 tracks_6|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|y_axis_values: True tracks_2|track_file_style_conditional|min_value: 1 tracks_3|track_file_style_conditional|logScale_conditional|log_pseudocount: 2 tracks_1|track_file_style_conditional|grid: True tracks_3|track_file_style_conditional|color: green tracks_2|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_4|track_file_style_conditional|height_bedgraph: 5 tracks_3|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_6|track_file_style_conditional|op|operation: log2(1+file) tracks_0|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|show_data: True tracks_7|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_2|track_file_style_conditional|color: red tracks_4|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|color: blue tracks_7|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_1|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_2|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original tracks_2|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|height_bedgraph: 5 tracks_8|track_file_style_conditional|xaxis_where: bottom tracks_3|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 tracks_6|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|min_value: 0.7 tracks_0|track_file_style_conditional|height_bedgraph: 5 tracks_0|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_5|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_7|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_0|track_file_style_conditional|show_data: True tracks_1|track_file_style_conditional|show_data: True tracks_6|track_file_style_conditional|title: bedgraph color = black operation = log2(1+file) min_value = 0 region: chr2:73,800,000-75,744,000 tracks_6|track_file_style_conditional|grid: True tracks_1|track_file_style_conditional|title: bedgraph color = blue transform = log tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_6|track_file_style_conditional|min_value: 0 tracks_3|track_file_style_conditional|title: bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 tracks_0|track_file_style_conditional|grid: True tracks_5|track_file_style_conditional|color: black tracks_5|track_file_style_conditional|min_value: 0 tracks_4|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|color: black tracks_7|track_file_style_conditional|grid: True |
attributes: name |
GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz name |
Test-20 |
tracks_8|track_file_style_conditional|line_width: 3 tracks_2|track_file_style_conditional|transform: log1p tracks_6|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_9|track_file_style_conditional|track_file_style_selector: vlines_track_option tracks_8|track_file_style_conditional|track_file_style_selector: link_track_option tracks_2|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_4|track_file_style_conditional|track_file_style_selector: link_track_option image_file_format: png tracks_9|track_file_style_conditional|track_input_bed_single: tad_classification.bed tracks_2|track_file_style_conditional|title: depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) tracks_7|track_file_style_conditional|links_type: loops tracks_4|track_file_style_conditional|title: links line_width = 3 color RdYlGn tracks_2|track_file_style_conditional|show_masked_bins: False tracks_6|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_1|track_file_style_conditional|spacer_height: 0.05 tracks_1|track_file_style_conditional|track_file_style_selector: spacer_option tracks_8|track_file_style_conditional|invert_orientation: True tracks_8|track_file_style_conditional|color_link|color: RdYlGn tracks_2|track_file_style_conditional|min_value: 5 tracks_7|track_file_style_conditional|color_link|color: red tracks_3|track_file_style_conditional|track_input_link: test_wide.arcs tracks_4|track_file_style_conditional|track_input_link: test_wide.arcs tracks_5|track_file_style_conditional|spacer_height: 1 tracks_2|track_file_style_conditional|depth: 300000 tracks_4|track_file_style_conditional|invert_orientation: True tracks_7|track_file_style_conditional|overlay_select: share-y tracks_9|track_file_style_conditional|line_width: 3 tracks_3|track_file_style_conditional|overlay_select: share-y tracks_8|track_file_style_conditional|use_middle: true tracks_7|track_file_style_conditional|track_file_style_selector: link_track_option tracks_8|track_file_style_conditional|title: links line_width = 3 color RdYlGn use_middle = true tracks_7|track_file_style_conditional|track_input_link: test_wide.arcs tracks_5|track_file_style_conditional|track_file_style_selector: spacer_option tracks_3|track_file_style_conditional|line_width: 5 tracks_6|track_file_style_conditional|depth: 300000 tracks_2|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_4|track_file_style_conditional|color_link|color: RdYlGn tracks_8|track_file_style_conditional|track_input_link: test_wide.arcs tracks_3|track_file_style_conditional|color_link|color: red tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option tracks_6|track_file_style_conditional|title: depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) region: chrX:3000000-3300000 tracks_6|track_file_style_conditional|show_masked_bins: False tracks_4|track_file_style_conditional|line_width: 3 tracks_0|track_file_style_conditional|xaxis_where: top tracks_7|track_file_style_conditional|line_width: 5 tracks_6|track_file_style_conditional|transform: log1p tracks_6|track_file_style_conditional|min_value: 5 tracks_3|track_file_style_conditional|links_type: loops |
attributes: name |
Li_et_al_2015.h5 test_wide.arcs tad_classification.bed name |