| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6 |
| toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.5 |
| 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 | 3.8 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
region: chrX:3000000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_1|track_file_style_conditional|depth: 200000 tracks_1|track_file_style_conditional|transform: log1p tracks_1|track_file_style_conditional|boundaries_file: domains.bed tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_2|track_file_style_conditional|spacer_height: 0.05 tracks_2|track_file_style_conditional|track_file_style_selector: spacer_option tracks_3|track_file_style_conditional|title: TAD state tracks_3|track_file_style_conditional|track_input_bed: tad_classification.bed tracks_3|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_3|track_file_style_conditional|height_chrom: 0.5 tracks_3|track_file_style_conditional|labels: False tracks_3|track_file_style_conditional|track_file_style_selector: chrom_states_option tracks_4|track_file_style_conditional|title: TAD separation score (Ramirez et al.) tracks_4|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz tracks_4|track_file_style_conditional|height_bedgraph: 10 tracks_4|track_file_style_conditional|type|type_selector: matrix tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option tracks_5|track_file_style_conditional|spacer_height: 1 tracks_5|track_file_style_conditional|track_file_style_selector: spacer_option tracks_6|track_file_style_conditional|title: bedgraph tracks_6|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_6|track_file_style_conditional|color: blue tracks_6|track_file_style_conditional|height_bedgraph: 4 tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_7|track_file_style_conditional|title: rep 1 test fill tracks_7|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_7|track_file_style_conditional|color: blue tracks_7|track_file_style_conditional|height_bigwig: 4 tracks_7|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_7|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_8|track_file_style_conditional|title: rep 1 test line tracks_8|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_8|track_file_style_conditional|color: red tracks_8|track_file_style_conditional|height_bigwig: 4 tracks_8|track_file_style_conditional|type_conditional|width_line: 1 tracks_8|track_file_style_conditional|type_conditional|type_selector: line_option tracks_8|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_9|track_file_style_conditional|title: rep 1 test lw=0.2 tracks_9|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_9|track_file_style_conditional|color: red tracks_9|track_file_style_conditional|height_bigwig: 4 tracks_9|track_file_style_conditional|type_conditional|width_line: 0.1 tracks_9|track_file_style_conditional|type_conditional|type_selector: line_option tracks_9|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_10|track_file_style_conditional|title: rep 1 test point:0.5 tracks_10|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_10|track_file_style_conditional|color: black tracks_10|track_file_style_conditional|height_bigwig: 4 tracks_10|track_file_style_conditional|type_conditional|width_point: 0.5 tracks_10|track_file_style_conditional|type_conditional|type_selector: point_option tracks_10|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_11|track_file_style_conditional|spacer_height: 0.5 tracks_11|track_file_style_conditional|track_file_style_selector: spacer_option tracks_12|track_file_style_conditional|title: genes tracks_12|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_12|track_file_style_conditional|height_bed: 5 tracks_12|track_file_style_conditional|labels|fontsize: 10 tracks_12|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_13|track_file_style_conditional|spacer_height: 1 tracks_13|track_file_style_conditional|track_file_style_selector: spacer_option tracks_14|track_file_style_conditional|title: max num rows 3 tracks_14|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_14|track_file_style_conditional|height_bed: 3 tracks_14|track_file_style_conditional|labels|fontsize: 8 tracks_14|track_file_style_conditional|bed_style|bed_advanced|gene_rows: 3 tracks_14|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_15|track_file_style_conditional|spacer_height: 1 tracks_15|track_file_style_conditional|track_file_style_selector: spacer_option tracks_16|track_file_style_conditional|title: bed6 global max row tracks_16|track_file_style_conditional|track_input_bed: dm3_genes.bed6.gz tracks_16|track_file_style_conditional|height_bed: 20 tracks_16|track_file_style_conditional|labels|fontsize: 10 tracks_16|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_16|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_17|track_file_style_conditional|track_input_bed_single: domains.bed tracks_17|track_file_style_conditional|track_file_style_selector: vlines_track_option image_file_format: png |
name: value |
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 value |
| Test-2 |
region: chrX:3000000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: rep bed tracks_1|track_file_style_conditional|track_input_bedgraph: ['bedgraph_chrx_2e6_5e6.bg', 'bedgraph2_X_2.5e6_3.5e6.bdg', 'tad_score.gz'] tracks_1|track_file_style_conditional|type_conditional|width_point: 2 tracks_1|track_file_style_conditional|type_conditional|type_selector: point_option tracks_1|track_file_style_conditional|show_data: True tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_2|track_file_style_conditional|title: rep 1 test line tracks_2|track_file_style_conditional|track_input_bigwig: ['bigwig_chrx_2e6_5e6.bw', 'bigwig_chrx_2e6_5e6.bw'] tracks_2|track_file_style_conditional|color: red tracks_2|track_file_style_conditional|height_bigwig: 4 tracks_2|track_file_style_conditional|type_conditional|width_line: 1 tracks_2|track_file_style_conditional|type_conditional|type_selector: line_option tracks_2|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_3|track_file_style_conditional|title: nans_to_zeros tracks_3|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_3|track_file_style_conditional|color: blue tracks_3|track_file_style_conditional|height_bigwig: 4 tracks_3|track_file_style_conditional|reading_bw_conditional|nans_to_zeros: True tracks_3|track_file_style_conditional|type_conditional|width_line: 1 tracks_3|track_file_style_conditional|type_conditional|type_selector: line_option tracks_3|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_4|track_file_style_conditional|title: tracks_4|track_file_style_conditional|y_values: 50 tracks_4|track_file_style_conditional|color: orange tracks_4|track_file_style_conditional|line_width: 2 tracks_4|track_file_style_conditional|line_style: dashed tracks_4|track_file_style_conditional|overlay_select: share-y tracks_4|track_file_style_conditional|track_file_style_selector: hlines_track_option tracks_5|track_file_style_conditional|title: hlines tracks_5|track_file_style_conditional|y_values: 0, 10, 20, 100 tracks_5|track_file_style_conditional|color: purple tracks_5|track_file_style_conditional|min_value: 12 tracks_5|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|invert_orientation: True tracks_5|track_file_style_conditional|track_file_style_selector: hlines_track_option image_file_format: png |
name: value |
bedgraph_chrx_2e6_5e6.bg bedgraph2_X_2.5e6_3.5e6.bdg tad_score.gz bigwig_chrx_2e6_5e6.bw bigwig_chrx_2e6_5e6.bw value |
| Test-3 |
region: chrX:3000000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) log1p tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_1|track_file_style_conditional|colormap: RdYlBu_r tracks_1|track_file_style_conditional|depth: 200000 tracks_1|track_file_style_conditional|transform: log1p tracks_1|track_file_style_conditional|boundaries_file: domains.bed tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_2|track_file_style_conditional|title: TAD state tracks_2|track_file_style_conditional|track_input_bed: tad_classification.bed tracks_2|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_2|track_file_style_conditional|height_chrom: 0.5 tracks_2|track_file_style_conditional|labels: False tracks_2|track_file_style_conditional|track_file_style_selector: chrom_states_option tracks_3|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) inverted no transform tracks_3|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_3|track_file_style_conditional|colormap: Reds tracks_3|track_file_style_conditional|min_value: 5 tracks_3|track_file_style_conditional|max_value: 70 tracks_3|track_file_style_conditional|depth: 200000 tracks_3|track_file_style_conditional|transform: no tracks_3|track_file_style_conditional|invert_orientation: True tracks_3|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_4|track_file_style_conditional|spacer_height: 1 tracks_4|track_file_style_conditional|track_file_style_selector: spacer_option tracks_5|track_file_style_conditional|title: bedgraph with negative values tracks_5|track_file_style_conditional|track_input_bedgraph: test_with_neg_values.bg.gz tracks_5|track_file_style_conditional|color: black tracks_5|track_file_style_conditional|color_negative|color: red tracks_5|track_file_style_conditional|color_negative|color_negative_select: true tracks_5|track_file_style_conditional|height_bedgraph: 4 tracks_5|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_6|track_file_style_conditional|title: bedgraph tracks_6|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_6|track_file_style_conditional|color: blue tracks_6|track_file_style_conditional|height_bedgraph: 4 tracks_6|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_7|track_file_style_conditional|title: rep 1 test fill tracks_7|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_7|track_file_style_conditional|color: blue tracks_7|track_file_style_conditional|height_bigwig: 4 tracks_7|track_file_style_conditional|type_conditional|type_selector: fill_option tracks_7|track_file_style_conditional|track_file_style_selector: bigwig_track_option 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|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_8|track_file_style_conditional|color: red tracks_8|track_file_style_conditional|height_bigwig: 10 tracks_8|track_file_style_conditional|reading_bw_conditional|summary_method: max tracks_8|track_file_style_conditional|reading_bw_conditional|number_of_bins: 100 tracks_8|track_file_style_conditional|type_conditional|width_point: 5 tracks_8|track_file_style_conditional|type_conditional|type_selector: point_option tracks_8|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_9|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_9|track_file_style_conditional|color: #c00000 tracks_9|track_file_style_conditional|height_bigwig: 10 tracks_9|track_file_style_conditional|reading_bw_conditional|summary_method: min tracks_9|track_file_style_conditional|type_conditional|type_selector: line_option tracks_9|track_file_style_conditional|overlay_select: share-y tracks_9|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_10|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_10|track_file_style_conditional|color: black tracks_10|track_file_style_conditional|height_bigwig: 10 tracks_10|track_file_style_conditional|reading_bw_conditional|summary_method: min tracks_10|track_file_style_conditional|reading_bw_conditional|number_of_bins: 30000 tracks_10|track_file_style_conditional|type_conditional|type_selector: line_option tracks_10|track_file_style_conditional|overlay_select: share-y tracks_10|track_file_style_conditional|spacer_height: 1 tracks_10|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_11|track_file_style_conditional|title: genes in ucsc tracks_11|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_11|track_file_style_conditional|height_bed: 5 tracks_11|track_file_style_conditional|labels|fontsize: 10 tracks_11|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_11|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_12|track_file_style_conditional|title: bed6 global max row color from score tracks_12|track_file_style_conditional|track_input_bed: dm3_genes.bed6.gz tracks_12|track_file_style_conditional|color_bed|color: RdYlBu_r tracks_12|track_file_style_conditional|color_bed|min_value: 0 tracks_12|track_file_style_conditional|color_bed|max_value: 2 tracks_12|track_file_style_conditional|color_bed|color_bed_select: colormap tracks_12|track_file_style_conditional|height_bed: 20 tracks_12|track_file_style_conditional|labels|fontsize: 10 tracks_12|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_12|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_13|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=red tracks_13|track_file_style_conditional|track_input_bed: domains.bed tracks_13|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_13|track_file_style_conditional|border_color_bed|color: red tracks_13|track_file_style_conditional|border_color_bed|border_color_bed_select: manually tracks_13|track_file_style_conditional|height_bed: 2 tracks_13|track_file_style_conditional|labels|plot_labels: false tracks_13|track_file_style_conditional|display: interleaved tracks_13|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_14|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=bed_rgb tracks_14|track_file_style_conditional|track_input_bed: domains.bed tracks_14|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_14|track_file_style_conditional|border_color_bed|border_color_bed_select: bed_rgb tracks_14|track_file_style_conditional|height_bed: 2 tracks_14|track_file_style_conditional|labels|plot_labels: false tracks_14|track_file_style_conditional|display: interleaved tracks_14|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_15|track_file_style_conditional|title: domains.bed using the 9th field for colors interleaved border=none tracks_15|track_file_style_conditional|track_input_bed: domains.bed tracks_15|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_15|track_file_style_conditional|border_color_bed|border_color_bed_select: none tracks_15|track_file_style_conditional|height_bed: 2 tracks_15|track_file_style_conditional|labels|plot_labels: false tracks_15|track_file_style_conditional|display: interleaved tracks_15|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png |
name: value |
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 value |
| Test-4 |
region: X:2700000-3100000 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_0|track_file_style_conditional|color: #00b0f0 tracks_0|track_file_style_conditional|height_bigwig: 7 tracks_0|track_file_style_conditional|reading_bw_conditional|number_of_bins: 2000 tracks_0|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_1|track_file_style_conditional|title: tracks_1|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|color: #ff0000 tracks_1|track_file_style_conditional|alpha: 0.5 tracks_1|track_file_style_conditional|reading_bw_conditional|number_of_bins: 300 tracks_1|track_file_style_conditional|overlay_select: share-y tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_2|track_file_style_conditional|xaxis_where: bottom tracks_2|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
bigwig_chrx_2e6_5e6.bw value |
| Test-5 |
region: X:3000000-3300000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: test tracks_1|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|bed_style|bed_style_select: UCSC 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|title: test tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78_asbed4.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_2|track_file_style_conditional|spacer_height: 1 tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png |
name: value |
dm3_subset_BDGP5.78.gtf.gz dm3_subset_BDGP5.78_asbed4.bed.gz value |
| Test-6 |
region: X:2760000-2802000 tracks_0|track_file_style_conditional|title: box tracks_0|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_0|track_file_style_conditional|color: #9bbb59 tracks_0|track_file_style_conditional|height_narrow_peak: 4 tracks_0|track_file_style_conditional|display|use_summit: True tracks_0|track_file_style_conditional|display|display_selector: box tracks_0|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_1|track_file_style_conditional|title: box line_width = 2 tracks_1|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_1|track_file_style_conditional|color: #9bbb59 tracks_1|track_file_style_conditional|height_narrow_peak: 4 tracks_1|track_file_style_conditional|display|use_summit: True tracks_1|track_file_style_conditional|display|display_selector: box tracks_1|track_file_style_conditional|line_width: 2 tracks_1|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_2|track_file_style_conditional|title: peak width 3 tracks_2|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_2|track_file_style_conditional|color: #c0504d tracks_2|track_file_style_conditional|height_narrow_peak: 4 tracks_2|track_file_style_conditional|display|use_summit: True tracks_2|track_file_style_conditional|display|show_data: True tracks_2|track_file_style_conditional|display|width_adjust: 3 tracks_2|track_file_style_conditional|display|max_value: 50 tracks_2|track_file_style_conditional|display|display_selector: peak tracks_2|track_file_style_conditional|labels|show_labels: false tracks_2|track_file_style_conditional|spacer_height: 0.5 tracks_2|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_3|track_file_style_conditional|title: peak no data range tracks_3|track_file_style_conditional|track_input_narrow_peak: test2.narrowPeak tracks_3|track_file_style_conditional|color: #000000 tracks_3|track_file_style_conditional|height_narrow_peak: 4 tracks_3|track_file_style_conditional|display|use_summit: False tracks_3|track_file_style_conditional|display|show_data: False tracks_3|track_file_style_conditional|display|display_selector: peak tracks_3|track_file_style_conditional|track_file_style_selector: narrow_peak_track_option tracks_4|track_file_style_conditional|xaxis_where: bottom tracks_4|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
test2.narrowPeak value |
| Test-7 |
region: chrX:3300000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: gtf default tracks_1|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|title: gtf merge transcripts, use gene_name, red 0.75 UTR tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|bed_style|bed_advanced|height_utr: 0.75 tracks_2|track_file_style_conditional|bed_style|bed_advanced|color_utr|color: #ff0000 tracks_2|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: manually tracks_2|track_file_style_conditional|bed_style|bed_advanced|gtf|prefered_name: gene_name tracks_2|track_file_style_conditional|bed_style|bed_advanced|gtf|merge_transcripts|merge_overlapping_exons: False tracks_2|track_file_style_conditional|bed_style|bed_advanced|gtf|merge_transcripts|merge_transcripts_select: true tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_3|track_file_style_conditional|title: same but merge overlapping exons tracks_3|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_3|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|bed_style|bed_advanced|height_utr: 0.75 tracks_3|track_file_style_conditional|bed_style|bed_advanced|color_utr|color: #ff0000 tracks_3|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: manually tracks_3|track_file_style_conditional|bed_style|bed_advanced|gtf|prefered_name: gene_name tracks_3|track_file_style_conditional|bed_style|bed_advanced|gtf|merge_transcripts|merge_overlapping_exons: True tracks_3|track_file_style_conditional|bed_style|bed_advanced|gtf|merge_transcripts|merge_transcripts_select: true tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|title: genes with scores tracks_4|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_4|track_file_style_conditional|color_bed|color: cool_r tracks_4|track_file_style_conditional|color_bed|color_bed_select: colormap tracks_4|track_file_style_conditional|height_bed: 10 tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_5|track_file_style_conditional|title: genes with utr as bed_rgb tracks_5|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_5|track_file_style_conditional|height_bed: 10 tracks_5|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: bed_rgb tracks_5|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_6|track_file_style_conditional|title: genes with coding as bed_rgb - labels_in_margin tracks_6|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_6|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_6|track_file_style_conditional|height_bed: 10 tracks_6|track_file_style_conditional|labels|labels_in_margin: True tracks_6|track_file_style_conditional|labels|plot_labels: true tracks_6|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_7|track_file_style_conditional|title: genes bed_rgb like - all_labels_inside tracks_7|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz tracks_7|track_file_style_conditional|color_bed|color_bed_select: bed_rgb tracks_7|track_file_style_conditional|height_bed: 10 tracks_7|track_file_style_conditional|labels|all_labels_inside: True tracks_7|track_file_style_conditional|labels|plot_labels: true tracks_7|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: like tracks_7|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png |
name: value |
dm3_subset_BDGP5.78.gtf.gz dm3_genes_withrgbandscore.bed.gz value |
| Test-8 |
region: chrX:3300000-3500000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: dm3_genes.bed tracks_1|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|bed_style|bed_advanced|global_max_row: True tracks_1|track_file_style_conditional|bed_style|bed_advanced|max_labels: 15 tracks_1|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|title: genes.bed.gz tracks_2|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|bed_style|bed_advanced|arrow_interval: 10 tracks_2|track_file_style_conditional|bed_style|bed_advanced|line_width: 2 tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png |
name: value |
dm3_genes.bed.gz value |
| Test-9 |
region: X:3133000-3138000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: defaut arrowhead fontstyle italic tracks_1|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|labels|fontstyle: italic 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|title: arrowhead_fraction 0.1 fontstyle oblique tracks_2|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|labels|fontstyle: oblique tracks_2|track_file_style_conditional|bed_style|arrowhead_fraction: 0.1 tracks_2|track_file_style_conditional|spacer_height: 1 tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_3|track_file_style_conditional|title: genes without orientation tracks_3|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78_asbed4.bed.gz tracks_3|track_file_style_conditional|color_bed|color: red tracks_3|track_file_style_conditional|color_bed|color_bed_select: manually tracks_3|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_3|track_file_style_conditional|spacer_height: 1 tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|title: arrowhead included tracks_4|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.gz tracks_4|track_file_style_conditional|color_bed|color: red tracks_4|track_file_style_conditional|color_bed|color_bed_select: manually tracks_4|track_file_style_conditional|height_bed: 10 tracks_4|track_file_style_conditional|bed_style|arrowhead_included: True tracks_4|track_file_style_conditional|spacer_height: 1 tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_5|track_file_style_conditional|track_input_bed_single: dm3_subset_BDGP5.78_asbed4.bed.gz tracks_5|track_file_style_conditional|line_width: 2 tracks_5|track_file_style_conditional|color: red tracks_5|track_file_style_conditional|zorder: 100 tracks_5|track_file_style_conditional|track_file_style_selector: vlines_track_option tracks_6|track_file_style_conditional|track_input_bed_single: dm3_genes_end.bed tracks_6|track_file_style_conditional|line_width: 5 tracks_6|track_file_style_conditional|line_style: solid tracks_6|track_file_style_conditional|color: blue tracks_6|track_file_style_conditional|zorder: -100 tracks_6|track_file_style_conditional|track_file_style_selector: vlines_track_option image_file_format: png |
name: value |
dm3_subset_BDGP5.78.gtf.gz dm3_subset_BDGP5.78_asbed4.bed.gz dm3_genes_end.bed value |
| Test-10 |
region: X:3340000-3380000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|track_input_bed: domains.bed tracks_1|track_file_style_conditional|color_bed|color: yellow tracks_1|track_file_style_conditional|color_bed|color_bed_select: manually tracks_1|track_file_style_conditional|height_bed: 6 tracks_1|track_file_style_conditional|display: triangles 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|title: bedgraph tracks_2|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_2|track_file_style_conditional|color: blue tracks_2|track_file_style_conditional|height_bedgraph: 4 tracks_2|track_file_style_conditional|type_conditional|type_selector: line_option tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|title: bedgraph tracks_3|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_3|track_file_style_conditional|color: blue tracks_3|track_file_style_conditional|height_bedgraph: 4 tracks_3|track_file_style_conditional|type_conditional|type_selector: line_option tracks_3|track_file_style_conditional|use_middle: True tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option image_file_format: png |
name: value |
domains.bed bedgraph_chrx_2e6_5e6.bg value |
| Test-11 |
region: chrX:3250000-3400000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_1|track_file_style_conditional|depth: 100000 tracks_1|track_file_style_conditional|transform: log1p tracks_1|track_file_style_conditional|show_masked_bins: True tracks_1|track_file_style_conditional|scale_factor: 2.0 tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_2|track_file_style_conditional|spacer_height: 0.05 tracks_2|track_file_style_conditional|track_file_style_selector: spacer_option tracks_3|track_file_style_conditional|title: TAD separation score (Ramirez et al.) as block with horizontal lines and data range tracks_3|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz tracks_3|track_file_style_conditional|height_bedgraph: 10 tracks_3|track_file_style_conditional|type|plot_horizontal_lines: True tracks_3|track_file_style_conditional|type|show_data: True tracks_3|track_file_style_conditional|type|pos_score_in_bin: block tracks_3|track_file_style_conditional|type|type_selector: lines tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option tracks_4|track_file_style_conditional|title: TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue tracks_4|track_file_style_conditional|track_input_bedgraph_matrix: tad_score.gz tracks_4|track_file_style_conditional|height_bedgraph: 10 tracks_4|track_file_style_conditional|type|plot_horizontal_lines: False tracks_4|track_file_style_conditional|type|pos_score_in_bin: center tracks_4|track_file_style_conditional|type|individual_color: blue tracks_4|track_file_style_conditional|type|summary_color: red tracks_4|track_file_style_conditional|type|type_selector: lines tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_matrix_track_option image_file_format: png |
name: value |
Li_et_al_2015.h5 tad_score.gz value |
| Test-12 |
region: chrX:3000000-3300000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: Kc DpnII (Li et al. 2015) tracks_1|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_1|track_file_style_conditional|colormap: Purples tracks_1|track_file_style_conditional|depth: 190000 tracks_1|track_file_style_conditional|transform: no tracks_1|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_2|track_file_style_conditional|title: tracks_2|track_file_style_conditional|track_input_link: test.arcs tracks_2|track_file_style_conditional|color_link|color: red tracks_2|track_file_style_conditional|color_link|color_link_select: manually tracks_2|track_file_style_conditional|line_width: 10 tracks_2|track_file_style_conditional|display|links_type: loops tracks_2|track_file_style_conditional|overlay_select: share-y tracks_2|track_file_style_conditional|track_file_style_selector: link_track_option tracks_3|track_file_style_conditional|title: tracks_3|track_file_style_conditional|track_input_link: test.arcs tracks_3|track_file_style_conditional|color_link|color: hot tracks_3|track_file_style_conditional|color_link|color_link_select: colormap tracks_3|track_file_style_conditional|height: 5 tracks_3|track_file_style_conditional|max_value: 5 tracks_3|track_file_style_conditional|invert_orientation: True tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option image_file_format: png |
name: value |
Li_et_al_2015.h5 test.arcs value |
| Test-13 |
region: chrX:3000000-3300000 tracks_0|track_file_style_conditional|title: default tracks_0|track_file_style_conditional|track_input_link: test.arcs tracks_0|track_file_style_conditional|color_link|color: #000000 tracks_0|track_file_style_conditional|color_link|color_link_select: manually tracks_0|track_file_style_conditional|track_file_style_selector: link_track_option tracks_1|track_file_style_conditional|title: ylim 20kb tracks_1|track_file_style_conditional|track_input_link: test.arcs tracks_1|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|display|ylim: 20000 tracks_1|track_file_style_conditional|track_file_style_selector: link_track_option tracks_2|track_file_style_conditional|title: compacted tracks_2|track_file_style_conditional|track_input_link: test.arcs tracks_2|track_file_style_conditional|color_link|color: #000000 tracks_2|track_file_style_conditional|color_link|color_link_select: manually tracks_2|track_file_style_conditional|display|compact_arcs_level: 1 tracks_2|track_file_style_conditional|track_file_style_selector: link_track_option tracks_3|track_file_style_conditional|title: highly compacted tracks_3|track_file_style_conditional|track_input_link: ['test.arcs', 'test.arcs'] tracks_3|track_file_style_conditional|color_link|color: #000000 tracks_3|track_file_style_conditional|color_link|color_link_select: manually tracks_3|track_file_style_conditional|display|compact_arcs_level: 2 tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option image_file_format: png |
name: value |
test.arcs test.arcs value |
| Test-14 |
region: chrX:3000000-3300000 global_args|title: Scale bar global_args|trackLabelFraction: 0.5 global_args|trackLabelHAlign: center tracks_0|track_file_style_conditional|spacer_height: 1.0 tracks_0|track_file_style_conditional|track_file_style_selector: spacer_option tracks_1|track_file_style_conditional|title: default tracks_1|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|track_file_style_selector: scale_bar_option 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|color: red tracks_2|track_file_style_conditional|alpha: 0.5 tracks_2|track_file_style_conditional|line_width: 2 tracks_2|track_file_style_conditional|scalebar_pos|x_center: 3200000 tracks_2|track_file_style_conditional|scalebar_pos|size: 100002 tracks_2|track_file_style_conditional|sb_where: right tracks_2|track_file_style_conditional|fontsize: 8 tracks_2|track_file_style_conditional|spacer_height: 4 tracks_2|track_file_style_conditional|track_file_style_selector: scale_bar_option image_file_format: png |
name: value |
value |
| Test-15 |
region: chrX:3300000-3500000 tracks_0|track_file_style_conditional|xaxis_where: bottom tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: flybase backbone blue tracks_1|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_1|track_file_style_conditional|height_bed: 10 tracks_1|track_file_style_conditional|bed_style|bed_advanced|backbone_color_bed|color: blue tracks_1|track_file_style_conditional|bed_style|bed_advanced|backbone_color_bed|backbone_color_bed_select: manually tracks_1|track_file_style_conditional|bed_style|bed_style_select: flybase tracks_1|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_2|track_file_style_conditional|title: UCSC backbone blue tracks_2|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_2|track_file_style_conditional|height_bed: 10 tracks_2|track_file_style_conditional|bed_style|bed_advanced|arrow_interval: 10 tracks_2|track_file_style_conditional|bed_style|bed_advanced|backbone_color_bed|color: blue tracks_2|track_file_style_conditional|bed_style|bed_advanced|backbone_color_bed|backbone_color_bed_select: manually tracks_2|track_file_style_conditional|bed_style|bed_style_select: UCSC tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_3|track_file_style_conditional|title: tssarrow tracks_3|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_3|track_file_style_conditional|height_bed: 10 tracks_3|track_file_style_conditional|bed_style|bed_style_select: tssarrow tracks_3|track_file_style_conditional|track_file_style_selector: gene_track_option tracks_4|track_file_style_conditional|title: tssarrow 5kb tracks_4|track_file_style_conditional|track_input_bed: dm3_genes.bed.gz tracks_4|track_file_style_conditional|height_bed: 10 tracks_4|track_file_style_conditional|bed_style|bed_advanced|arrow_length: 5000 tracks_4|track_file_style_conditional|bed_style|bed_style_select: tssarrow tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option image_file_format: png |
name: value |
dm3_genes.bed.gz value |
| Test-16 |
region: X:2700000-3100000 global_args|decreasingXAxis: True 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_0|track_file_style_conditional|color: #00b0f0 tracks_0|track_file_style_conditional|height_bigwig: 7 tracks_0|track_file_style_conditional|reading_bw_conditional|number_of_bins: 2000 tracks_0|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_1|track_file_style_conditional|title: tracks_1|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw tracks_1|track_file_style_conditional|color: #ff0000 tracks_1|track_file_style_conditional|alpha: 0.5 tracks_1|track_file_style_conditional|reading_bw_conditional|number_of_bins: 300 tracks_1|track_file_style_conditional|overlay_select: share-y tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option tracks_2|track_file_style_conditional|xaxis_where: bottom tracks_2|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
bigwig_chrx_2e6_5e6.bw value |
| Test-17 |
region: chr2:73,800,000-75,744,000 tracks_0|track_file_style_conditional|title: bedgraph color = blue transform = no tracks_0|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_0|track_file_style_conditional|color: blue tracks_0|track_file_style_conditional|height_bedgraph: 5 tracks_0|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|title: bedgraph color = blue transform = log tracks_1|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|height_bedgraph: 5 tracks_1|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_1|track_file_style_conditional|show_data: True tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_2|track_file_style_conditional|title: bedgraph color = red transform = log min_value = 1 tracks_2|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_2|track_file_style_conditional|color: red tracks_2|track_file_style_conditional|min_value: 1 tracks_2|track_file_style_conditional|height_bedgraph: 5 tracks_2|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_2|track_file_style_conditional|show_data: True tracks_2|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_3|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_3|track_file_style_conditional|color: green tracks_3|track_file_style_conditional|min_value: 0 tracks_3|track_file_style_conditional|height_bedgraph: 5 tracks_3|track_file_style_conditional|logScale_conditional|log_pseudocount: 2 tracks_3|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_3|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option 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_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_4|track_file_style_conditional|color: green tracks_4|track_file_style_conditional|min_value: 0.7 tracks_4|track_file_style_conditional|height_bedgraph: 5 tracks_4|track_file_style_conditional|op|operation: log(2+file) tracks_4|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 tracks_5|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_5|track_file_style_conditional|color: black tracks_5|track_file_style_conditional|min_value: 0 tracks_5|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_5|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_5|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_6|track_file_style_conditional|title: bedgraph color = black operation = log2(1+file) min_value = 0 tracks_6|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|color: black tracks_6|track_file_style_conditional|min_value: 0 tracks_6|track_file_style_conditional|height_bedgraph: 5 tracks_6|track_file_style_conditional|op|operation: log2(1+file) tracks_6|track_file_style_conditional|show_data: True tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_7|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original tracks_7|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|color: black tracks_7|track_file_style_conditional|min_value: 0 tracks_7|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_7|track_file_style_conditional|logScale_conditional|y_axis_values: True tracks_7|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_7|track_file_style_conditional|show_data: True tracks_7|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_8|track_file_style_conditional|xaxis_where: bottom tracks_8|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz value |
| Test-18 |
region: chrX:2700000-3100000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|title: file summary_method = mean number_of_bins=20 tracks_1|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|min_value: 0 tracks_1|track_file_style_conditional|max_value: 30 tracks_1|track_file_style_conditional|height_bedgraph: 4 tracks_1|track_file_style_conditional|reading_bdg_as_bw|summary_method: mean tracks_1|track_file_style_conditional|reading_bdg_as_bw|number_of_bins: 20 tracks_1|track_file_style_conditional|show_data: True tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_2|track_file_style_conditional|title: second_file summary_method = mean 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_2|track_file_style_conditional|min_value: 0 tracks_2|track_file_style_conditional|max_value: 30 tracks_2|track_file_style_conditional|height_bedgraph: 4 tracks_2|track_file_style_conditional|reading_bdg_as_bw|summary_method: mean tracks_2|track_file_style_conditional|show_data: True tracks_2|track_file_style_conditional|spacer_height: 0.5 tracks_2|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_3|track_file_style_conditional|title: operation = log1p(file) (no summary_method) tracks_3|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_3|track_file_style_conditional|color: blue tracks_3|track_file_style_conditional|height_bedgraph: 4 tracks_3|track_file_style_conditional|op|operation: log1p(file) tracks_3|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|spacer_height: 0.5 tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_4|track_file_style_conditional|title: operation = file - second_file tracks_4|track_file_style_conditional|track_input_bedgraph: bedgraph_chrx_2e6_5e6.bg tracks_4|track_file_style_conditional|color: blue tracks_4|track_file_style_conditional|color_negative|color: red tracks_4|track_file_style_conditional|color_negative|color_negative_select: true tracks_4|track_file_style_conditional|min_value: -30 tracks_4|track_file_style_conditional|max_value: 30 tracks_4|track_file_style_conditional|height_bedgraph: 8 tracks_4|track_file_style_conditional|op|operation: file - second_file tracks_4|track_file_style_conditional|op|second_file: bedgraph2_X_2.5e6_3.5e6.bdg tracks_4|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option image_file_format: png |
name: value |
bedgraph_chrx_2e6_5e6.bg bedgraph2_X_2.5e6_3.5e6.bdg value |
| Test-19 |
region: chr2:73,800,000-75,744,000 tracks_0|track_file_style_conditional|title: bedgraph color = blue transform = no tracks_0|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_0|track_file_style_conditional|color: blue tracks_0|track_file_style_conditional|height_bedgraph: 5 tracks_0|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|grid: True tracks_0|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|title: bedgraph color = blue transform = log tracks_1|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_1|track_file_style_conditional|color: blue tracks_1|track_file_style_conditional|height_bedgraph: 5 tracks_1|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_1|track_file_style_conditional|show_data: True tracks_1|track_file_style_conditional|grid: True tracks_1|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_2|track_file_style_conditional|title: bedgraph color = red transform = log min_value = 1 tracks_2|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_2|track_file_style_conditional|color: red tracks_2|track_file_style_conditional|min_value: 1 tracks_2|track_file_style_conditional|height_bedgraph: 5 tracks_2|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_2|track_file_style_conditional|show_data: True tracks_2|track_file_style_conditional|grid: True tracks_2|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_3|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_3|track_file_style_conditional|color: green tracks_3|track_file_style_conditional|min_value: 0 tracks_3|track_file_style_conditional|height_bedgraph: 5 tracks_3|track_file_style_conditional|logScale_conditional|log_pseudocount: 2 tracks_3|track_file_style_conditional|logScale_conditional|transform_selector: log tracks_3|track_file_style_conditional|show_data: True tracks_3|track_file_style_conditional|grid: True tracks_3|track_file_style_conditional|track_file_style_selector: bedgraph_track_option 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_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_4|track_file_style_conditional|color: green tracks_4|track_file_style_conditional|min_value: 0.7 tracks_4|track_file_style_conditional|height_bedgraph: 5 tracks_4|track_file_style_conditional|op|operation: log(2+file) tracks_4|track_file_style_conditional|show_data: True tracks_4|track_file_style_conditional|grid: True tracks_4|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_5|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 tracks_5|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_5|track_file_style_conditional|color: black tracks_5|track_file_style_conditional|min_value: 0 tracks_5|track_file_style_conditional|height_bedgraph: 5 tracks_5|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_5|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_5|track_file_style_conditional|show_data: True tracks_5|track_file_style_conditional|grid: True tracks_5|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_6|track_file_style_conditional|title: bedgraph color = black operation = log2(1+file) min_value = 0 tracks_6|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_6|track_file_style_conditional|color: black tracks_6|track_file_style_conditional|min_value: 0 tracks_6|track_file_style_conditional|height_bedgraph: 5 tracks_6|track_file_style_conditional|op|operation: log2(1+file) tracks_6|track_file_style_conditional|show_data: True tracks_6|track_file_style_conditional|grid: True tracks_6|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_7|track_file_style_conditional|title: bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original tracks_7|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_7|track_file_style_conditional|color: black tracks_7|track_file_style_conditional|min_value: 0 tracks_7|track_file_style_conditional|height_bedgraph: 5 tracks_7|track_file_style_conditional|logScale_conditional|log_pseudocount: 1 tracks_7|track_file_style_conditional|logScale_conditional|y_axis_values: True tracks_7|track_file_style_conditional|logScale_conditional|transform_selector: log2 tracks_7|track_file_style_conditional|show_data: True tracks_7|track_file_style_conditional|grid: True tracks_7|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_8|track_file_style_conditional|xaxis_where: bottom tracks_8|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz value |
| Test-20 |
region: chrX:3000000-3300000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|spacer_height: 0.05 tracks_1|track_file_style_conditional|track_file_style_selector: spacer_option tracks_2|track_file_style_conditional|title: depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) tracks_2|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_2|track_file_style_conditional|min_value: 5 tracks_2|track_file_style_conditional|depth: 300000 tracks_2|track_file_style_conditional|transform: log1p tracks_2|track_file_style_conditional|show_masked_bins: False tracks_2|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_3|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|line_width: 5 tracks_3|track_file_style_conditional|display|links_type: loops tracks_3|track_file_style_conditional|overlay_select: share-y tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option tracks_4|track_file_style_conditional|title: links line_width = 3 color RdYlGn tracks_4|track_file_style_conditional|track_input_link: test_wide.arcs tracks_4|track_file_style_conditional|color_link|color: RdYlGn tracks_4|track_file_style_conditional|line_width: 3 tracks_4|track_file_style_conditional|height: 3 tracks_4|track_file_style_conditional|invert_orientation: True tracks_4|track_file_style_conditional|track_file_style_selector: link_track_option tracks_5|track_file_style_conditional|spacer_height: 1 tracks_5|track_file_style_conditional|track_file_style_selector: spacer_option tracks_6|track_file_style_conditional|title: depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) tracks_6|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_6|track_file_style_conditional|min_value: 5 tracks_6|track_file_style_conditional|depth: 300000 tracks_6|track_file_style_conditional|transform: log1p tracks_6|track_file_style_conditional|show_masked_bins: False tracks_6|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_7|track_file_style_conditional|track_input_link: test_wide.arcs tracks_7|track_file_style_conditional|color_link|color: red tracks_7|track_file_style_conditional|line_width: 5 tracks_7|track_file_style_conditional|display|links_type: loops tracks_7|track_file_style_conditional|overlay_select: share-y 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_8|track_file_style_conditional|track_input_link: test_wide.arcs tracks_8|track_file_style_conditional|color_link|color: RdYlGn tracks_8|track_file_style_conditional|line_width: 3 tracks_8|track_file_style_conditional|display|use_middle: true tracks_8|track_file_style_conditional|height: 3 tracks_8|track_file_style_conditional|invert_orientation: True tracks_8|track_file_style_conditional|track_file_style_selector: link_track_option tracks_9|track_file_style_conditional|track_input_bed_single: tad_classification.bed tracks_9|track_file_style_conditional|line_width: 3 tracks_9|track_file_style_conditional|track_file_style_selector: vlines_track_option image_file_format: png |
name: value |
Li_et_al_2015.h5 test_wide.arcs tad_classification.bed value |
| Test-21 |
region: X:3000000-3600000 global_args|dpi: 20 global_args|plotWidth: 12 global_args|trackLabelFraction: 0.3 tracks_0|track_file_style_conditional|title: scalebar where = right tracks_0|track_file_style_conditional|sb_where: right tracks_0|track_file_style_conditional|spacer_height: 0.5 tracks_0|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_1|track_file_style_conditional|title: scalebar scalebar_start_position = 3200000 tracks_1|track_file_style_conditional|scalebar_pos|scalebar_start_position: 3200000 tracks_1|track_file_style_conditional|spacer_height: 0.5 tracks_1|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_2|track_file_style_conditional|title: scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000 tracks_2|track_file_style_conditional|scalebar_pos|scalebar_start_position: 3200000 tracks_2|track_file_style_conditional|scalebar_pos|scalebar_end_position: 3250000 tracks_2|track_file_style_conditional|spacer_height: 0.5 tracks_2|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_3|track_file_style_conditional|title: scalebar scalebar_start_position = 3200000 x_center = 3250000 tracks_3|track_file_style_conditional|scalebar_pos|scalebar_start_position: 3200000 tracks_3|track_file_style_conditional|scalebar_pos|x_center: 3250000 tracks_3|track_file_style_conditional|spacer_height: 0.5 tracks_3|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_4|track_file_style_conditional|title: scalebar scalebar_start_position = 3200000 size = 50000 tracks_4|track_file_style_conditional|scalebar_pos|scalebar_start_position: 3200000 tracks_4|track_file_style_conditional|scalebar_pos|size: 50000 tracks_4|track_file_style_conditional|spacer_height: 0.5 tracks_4|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_5|track_file_style_conditional|title: scalebar scalebar_end_position = 3200000 size = 50000 tracks_5|track_file_style_conditional|scalebar_pos|scalebar_end_position: 3200000 tracks_5|track_file_style_conditional|scalebar_pos|size: 50000 tracks_5|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_6|track_file_style_conditional|xaxis_where: bottom tracks_6|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
value |
| Test-22 |
region: chrM:10-30 tracks_0|track_file_style_conditional|title: scalebar height = 5 tracks_0|track_file_style_conditional|sb_where: right tracks_0|track_file_style_conditional|height: 5 tracks_0|track_file_style_conditional|spacer_height: 0.5 tracks_0|track_file_style_conditional|track_file_style_selector: scale_bar_option tracks_1|track_file_style_conditional|fasta_source|fasta_cached: chrM tracks_1|track_file_style_conditional|fasta_source|fasta_source_selector: cached tracks_1|track_file_style_conditional|title: fasta from cached tracks_1|track_file_style_conditional|spacer_height: 0.5 tracks_1|track_file_style_conditional|track_file_style_selector: fasta_option tracks_2|track_file_style_conditional|fasta_source|fasta_local: chrM.fa tracks_2|track_file_style_conditional|fasta_source|fasta_source_selector: history tracks_2|track_file_style_conditional|title: fasta from history height = 5 tracks_2|track_file_style_conditional|height: 5 tracks_2|track_file_style_conditional|track_file_style_selector: fasta_option image_file_format: png |
name: value |
chrM.fa value |
| Test-23 |
region: chrX:3000000-3300000 tracks_0|track_file_style_conditional|xaxis_where: top tracks_0|track_file_style_conditional|track_file_style_selector: xaxis_option tracks_1|track_file_style_conditional|spacer_height: 0.05 tracks_1|track_file_style_conditional|track_file_style_selector: spacer_option tracks_2|track_file_style_conditional|title: classical depth=300000 with arcs tracks_2|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_2|track_file_style_conditional|depth: 300000 tracks_2|track_file_style_conditional|track_file_style_selector: hic_matrix_option tracks_3|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|line_width: 5 tracks_3|track_file_style_conditional|display|links_type: loops tracks_3|track_file_style_conditional|overlay_select: share-y tracks_3|track_file_style_conditional|track_file_style_selector: link_track_option tracks_4|track_file_style_conditional|title: square with arcs tracks_4|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_4|track_file_style_conditional|track_file_style_selector: hic_matrix_square_option tracks_5|track_file_style_conditional|track_input_link: test_wide.arcs tracks_5|track_file_style_conditional|color_link|color: red tracks_5|track_file_style_conditional|line_width: 5 tracks_5|track_file_style_conditional|display|links_type: squares tracks_5|track_file_style_conditional|overlay_select: share-y tracks_5|track_file_style_conditional|track_file_style_selector: link_track_option tracks_6|track_file_style_conditional|title: square with arcs region2=chrX:3000000-3100000 tracks_6|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_6|track_file_style_conditional|region2: chrX:3000000-3100000 tracks_6|track_file_style_conditional|track_file_style_selector: hic_matrix_square_option tracks_7|track_file_style_conditional|track_input_link: test_wide.arcs tracks_7|track_file_style_conditional|color_link|color: red tracks_7|track_file_style_conditional|line_width: 5 tracks_7|track_file_style_conditional|display|links_type: squares tracks_7|track_file_style_conditional|overlay_select: share-y tracks_7|track_file_style_conditional|track_file_style_selector: link_track_option tracks_8|track_file_style_conditional|title: square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000 tracks_8|track_file_style_conditional|matrix_h5_cooler_multiple: Li_et_al_2015.h5 tracks_8|track_file_style_conditional|colormap: Blues tracks_8|track_file_style_conditional|region2: chrX:3000000-3100000 tracks_8|track_file_style_conditional|transform: no tracks_8|track_file_style_conditional|boundaries_file: tad_classification.bed tracks_8|track_file_style_conditional|track_file_style_selector: hic_matrix_square_option image_file_format: png |
name: value |
Li_et_al_2015.h5 test_wide.arcs tad_classification.bed value |
| Test-24 |
region: 2:34704975-34705208 tracks_0|track_file_style_conditional|track_input_maf: first.maf tracks_0|track_file_style_conditional|title: default tracks_0|track_file_style_conditional|reference: mm10 tracks_0|track_file_style_conditional|spacer_height: 1 tracks_0|track_file_style_conditional|track_file_style_selector: maf_option tracks_1|track_file_style_conditional|track_input_maf: first.maf tracks_1|track_file_style_conditional|title: height = 3 show sequence tracks_1|track_file_style_conditional|height: 3 tracks_1|track_file_style_conditional|reference: mm10 tracks_1|track_file_style_conditional|display_ref_seq: True tracks_1|track_file_style_conditional|spacer_height: 1 tracks_1|track_file_style_conditional|track_file_style_selector: maf_option tracks_2|track_file_style_conditional|track_input_maf: first.maf tracks_2|track_file_style_conditional|title: species_order = hg19 rn5, species_labels = Human Rat tracks_2|track_file_style_conditional|height: 3 tracks_2|track_file_style_conditional|reference: mm10 tracks_2|track_file_style_conditional|species_order: hg19 rn5 tracks_2|track_file_style_conditional|species_labels: Human Rat tracks_2|track_file_style_conditional|spacer_height: 1 tracks_2|track_file_style_conditional|track_file_style_selector: maf_option tracks_3|track_file_style_conditional|track_input_maf: first.maf tracks_3|track_file_style_conditional|title: species_order = hg19, species_labels = Human, species_order_only = true tracks_3|track_file_style_conditional|height: 3 tracks_3|track_file_style_conditional|reference: mm10 tracks_3|track_file_style_conditional|species_order: hg19 tracks_3|track_file_style_conditional|species_labels: Human tracks_3|track_file_style_conditional|species_order_only: True tracks_3|track_file_style_conditional|spacer_height: 1 tracks_3|track_file_style_conditional|track_file_style_selector: maf_option tracks_4|track_file_style_conditional|xaxis_where: bottom tracks_4|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
first.maf value |
| Test-25 |
region: chr2:73,800,000-75,744,000 tracks_0|track_file_style_conditional|title: bedgraph color = blue tracks_0|track_file_style_conditional|track_input_bedgraph: GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz tracks_0|track_file_style_conditional|color: blue tracks_0|track_file_style_conditional|max_value: 5 tracks_0|track_file_style_conditional|height_bedgraph: 5 tracks_0|track_file_style_conditional|show_data: True tracks_0|track_file_style_conditional|track_file_style_selector: bedgraph_track_option tracks_1|track_file_style_conditional|track_input_bed_single: islands.bed tracks_1|track_file_style_conditional|track_file_style_selector: vhighlight_track_option tracks_2|track_file_style_conditional|xaxis_where: bottom tracks_2|track_file_style_conditional|track_file_style_selector: xaxis_option image_file_format: png |
name: value |
GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz islands.bed value |