Repository revision
10:a1abfa420d9d

Repository 'pygenometracks'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks

pyGenomeTracks tool metadata
Miscellaneous
plot genomic data tracks
pygenomeTracks
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6+galaxy1
3.6+galaxy1
pyGenomeTracks --version | tail -n 1
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6+galaxy1 (this tool)
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 3.6 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|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|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|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 1 test line
tracks_1|track_file_style_conditional|track_input_bigwig: ['bigwig_chrx_2e6_5e6.bw', 'bigwig_chrx_2e6_5e6.bw']
tracks_1|track_file_style_conditional|color: red
tracks_1|track_file_style_conditional|height_bigwig: 4
tracks_1|track_file_style_conditional|type_conditional|width_line: 1
tracks_1|track_file_style_conditional|type_conditional|type_selector: line_option
tracks_1|track_file_style_conditional|track_file_style_selector: bigwig_track_option
tracks_2|track_file_style_conditional|title: nans_to_zeros
tracks_2|track_file_style_conditional|track_input_bigwig: bigwig_chrx_2e6_5e6.bw
tracks_2|track_file_style_conditional|color: blue
tracks_2|track_file_style_conditional|height_bigwig: 4
tracks_2|track_file_style_conditional|reading_bw_conditional|nans_to_zeros: True
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|show_data: True
tracks_2|track_file_style_conditional|track_file_style_selector: bigwig_track_option
tracks_3|track_file_style_conditional|title:
tracks_3|track_file_style_conditional|y_values: 50
tracks_3|track_file_style_conditional|color: orange
tracks_3|track_file_style_conditional|line_width: 2
tracks_3|track_file_style_conditional|line_style: dashed
tracks_3|track_file_style_conditional|overlay_select: share-y
tracks_3|track_file_style_conditional|track_file_style_selector: hlines_track_option
tracks_4|track_file_style_conditional|title: hlines
tracks_4|track_file_style_conditional|y_values: 0, 10, 20, 100
tracks_4|track_file_style_conditional|color: purple
tracks_4|track_file_style_conditional|min_value: 12
tracks_4|track_file_style_conditional|show_data: True
tracks_4|track_file_style_conditional|invert_orientation: True
tracks_4|track_file_style_conditional|track_file_style_selector: hlines_track_option
image_file_format: png
name: value
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|depth: 200000
tracks_3|track_file_style_conditional|min_value: 5
tracks_3|track_file_style_conditional|max_value: 70
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|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|color_bed_select: colormap
tracks_12|track_file_style_conditional|height_bed: 20
tracks_12|track_file_style_conditional|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|fontsize: 10
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|fontsize: 10
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|fontsize: 10
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|show_labels: True
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|show_labels: True
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|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|show_labels: True
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: genes
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|track_file_style_selector: gene_track_option
tracks_2|track_file_style_conditional|title: gtf
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: True
tracks_2|track_file_style_conditional|track_file_style_selector: gene_track_option
tracks_3|track_file_style_conditional|title: genes with scores
tracks_3|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz
tracks_3|track_file_style_conditional|color_bed|color: cool_r
tracks_3|track_file_style_conditional|color_bed|color_bed_select: colormap
tracks_3|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|title: genes with utr as bed_rgb
tracks_4|track_file_style_conditional|track_input_bed: dm3_genes_withrgbandscore.bed.gz
tracks_4|track_file_style_conditional|height_bed: 10
tracks_4|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: bed_rgb
tracks_4|track_file_style_conditional|track_file_style_selector: gene_track_option
tracks_5|track_file_style_conditional|title: genes with coding as bed_rgb - labels_in_margin
tracks_5|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_5|track_file_style_conditional|height_bed: 10
tracks_5|track_file_style_conditional|labels|labels_in_margin: True
tracks_5|track_file_style_conditional|labels|plot_labels: true
tracks_5|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_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|all_labels_inside: True
tracks_6|track_file_style_conditional|labels|plot_labels: true
tracks_6|track_file_style_conditional|bed_style|bed_advanced|color_utr|color_utr_select: like
tracks_6|track_file_style_conditional|track_file_style_selector: gene_track_option
image_file_format: png
name: value
dm3_genes.bed.gz
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: 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|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|color_bed|color: red
tracks_2|track_file_style_conditional|color_bed|color_bed_select: manually
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
tracks_3|track_file_style_conditional|title: test
tracks_3|track_file_style_conditional|track_input_bed: dm3_subset_BDGP5.78.gtf.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|arrowhead_included: True
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|track_input_bed_single: dm3_subset_BDGP5.78_asbed4.bed.gz
tracks_4|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
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.)
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.)
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|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|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|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|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
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|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
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
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|track_file_style_selector: gene_track_option
tracks_2|track_file_style_conditional|title: UCSC
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_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|depth: 300000
tracks_2|track_file_style_conditional|min_value: 5
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|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|depth: 300000
tracks_6|track_file_style_conditional|min_value: 5
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|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|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|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: 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|spacer_height: 0.5
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