README for CisGenome Browser: A flexible tool for genomic data visualization
Running Time Directory Structure
signal track
region track
gene track
conservation track
genome sequence track
motif session
cel session
data plot sesson
Control CisGenome Browser by a Third Party Program
CisGenome Browser is an open source, platform independent tool which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs. It has features that are specifically designed for ultra high throughput sequencing data visualization.
CisGenome Browser runs on Windows, Linux and Mac platforms. The use of CisGenome Browser is very easy, and the interface is similar to other genome browsers, such as the UCSC Genome Browser. CisGenome Browser is suitable for visualizing microarray/sequencing/other biological data. It runs locally so that there is no need to upload the user data via internet like adding custom tracks when using UCSC Genome Browser or any other online browsers.
CisGenome Browser is designed to work with any other programs as a visualization component. It is integrated in CisGenome and JETTA. Here is a nice tutorial on CisGenome Browser written by Hongkai Ji..
For detailed instructions, see Getting Started.
1. Download the zipped files from its website.
2. Unzip the files to somewhere on the hard drive. If an old version is reviously installed, just unzip the files to the same directory to have the program files overwritten. All the user data will not be touched, and they will be automatically pre-loaded with the new version. To prevent unexpected damage, backup the files first.
3. Click display_server_pi.exe (or display_server.exe if you are using the old Windows only version) to run it. then a tray icon will automatically appear in the tray area. A dialog might pop up asking about blocking the program, just click "Unblock".
4. Right click it and choose "Browse" (double click the icon will do the same). A web page will be opened in your default browser.
5. In the web page, create new sessions or load old sessions, according to the manual.
6. play with it~
The above is for the Windows version. For the linux or Mac versions, follow the instructions given in the Getting Started.
Running Time Directory Structure
The default running time directory structure is as follows:
wwwroot
|
------sessions
|
------temp
|
------templates
The directory "wwwroot" contains the executable file display_server_pi.exe (or display_server.exe if you are using the old Windows only version).All the sessions files (*.ini) are in the "sessions" directory. The directory "templates" contains some necessary html templates that are used by the program. All the temporary files, mostly pictures, are in the "temp" directory.
Files in the "temp" directory can be deleted freely. Files in the "sessions" directory can be deleted if the corresponding sessions are no longer needed. Files in other directories should never be deleted.
For signal tracks, Affymetrix BAR file format (binary) or tab-delimited text file format are supported. The text files shoule be in the following format:
Chromosome[tab]Position[tab]value
For region tracks, UCSC BED format is partly supported (text).
It can also be only the first three columns, or add another column for signals.
For gene annotation tracks (for visualizing sequencing reads, you can use this type of track, just one read per line), UCSC refFlat format, UCSC BED format or the BAM format are supported.
Sample file in refFlat format. As another example, the refFlat format annotation file for hg19 can be downloaded at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
Sample file in BED format.
Notice that other gene annotations files downloaded from UCSC, such as knowGenes.txt and etc, are not in exactly the same format as the refFlat.txt, therefore manually converting to the refFlat format is needed before imported into CisGenome Browser.
For DNA sequences, first download .fa (FASTA) files from UCSC, then convert them to .sq files using CisGenome command line tools before imported into CisGenome Browser.
For conservation scores, similar to DNA sequences, download data from UCSC, convert them using CisGenome command line tools before imported into CisGenome Browser. For details, look at the User’s Manual of CisGenome.
For motif session, It should be text file containing the PSSM of the motif. An example file is here. For multiple motif file, current it only accepts the file that output by the motif sample "flex_module" in CisGenome. An example file is here.
For CEL session, it support CEL file formats from Affymetrix v1 to v5.
Control CisGenome Browser by a Third Party Program
CisGenome Browser can be easily controlled by a third party program regardless the programming language in which the program is written. The workflow for a third party program to control CisGenome Browser contains the following six steps:
The files in the "session" directory are in Windows INI format.
The file contain several sections, separated by section name lines in the format "[section_name]".
Each section contains several parameters, each in a line in the format "name=value", where "name" is the name of the parameter and "value" is the value of the parameter.
The first section is "[session]", which has the following possible parameters:
| parameter name | possible values | default values | note |
| type | genome, motif, cel, data | none | type of session. "genome" is for genome browser, "motif" is for motif logos, "cel" is for Affymetrix array image, and "data" is for general plot |
| seed | int | 0 | internal usage |
| refresh | 0 or 1 | false | refresh the page |
Depending on the type of the session, the second section can be "[genome]", "[motif]", "[cel]" or "[data]".
The "[genome]" section has the following possible parameters:
| parameter name | possible values | default values | note |
| num_tracks | int | 0 | number of tracks |
| num_hided_tracks | int | 0 | number of hiden tracks |
| region | genomic region | chr1:5001000-5002000 | genomic region |
| ucsc_genome_assembly | hg18, mm9, etc | none | genome assembly |
| pic_width | int | 800 | picture width |
| pic_margin | int | 15 | picture margin |
| font_size | int | 15 | font size |
| left_axis | 0 or 1 | 1 | show left axis |
| right_axis | 0 or 1 | 1 | show right axis |
| ucsc_browser | 0 or 1 | 0 | show UCSC genome browser |
| grid | gray, color, gray_shaded or color_shaded | gray | grid type |
| fold | integers separated by "," | none | folded tracks |
Depending on the number of tracks and hiden tracks, there will be several sections "[track1]", "[track2]", ..., "[hided_track1]", "[hided_track2]", etc. Each of these sections has the following possible parameters:
| parameter name | possible values | default values | note |
| title | string | none | track title |
| top_axis | 0 or 1 | 0 | show top axis |
| bottom_axis | 0 or 1 | 0 | show bottom axis |
| fast_draw | 0 or 1 | 1 | smart draw |
| pic_filename | string | none | picture file ame |
| type | gene, signal, conservation, region, nucleotide | none | track type |
| file_path | string | none | input file path, for track types "conservation" or "nucleotide" |
| pic_height | int | 100 | picture height, for track types "conservation", "signal" or "region" |
| plot_type | bar, heatmap, line or dot | 15 | type of plot, for track type"signal", track types "region" or "conservation" only has "bar" or "heatmap" |
| range_low | int | 0 | range lower bound, for track types "signal" or "region" |
| range_high | int | 0 | range upper bound, for track types "signal" or "region" |
| signal_width | int | 0 | signal width, for track type"signal" |
| zero_line | 0 or 1 | 0 | draw line at zero, for track types "signal" or "region" |
| always_include_zero | 0 or 1 | 1 | always include 0 in the range, for track types "signal" or "region" |
| max_draw_line_distance | int | 0 | maxum distance between lines, for track type "signal" |
| count_window | int | 0 | count data points in a window, for track type "signal" |
| src_filename | file names separated by "," | none | data file names, for track types "signal" or "region", track type "gene" only has one file name |
| color | black, red, blue, green, purple, pink, brown, orange or color code such as 0x004080 separated by "," | none | colors for data files, for track type "signal" or "region" |
| draw_exon_num | 0 or 1 | 0 | numbering exons, for track type "gene" |
| do_caching | 0 or 1 | 0 | cache the gene in memory, for track type "gene" |
| annotation | 0 or 1 | 1 | include track in search, for track type "gene" |
| max_height | int | 400 | maximum track height, for track type "gene" |
The "[motif]" section has the following possible parameters:
| parameter name | possible values | default values | note |
| multiple_motifs | 0 or 1 | 0 | draw multiple motifs |
| src_filename | string | none | data file name |
| pic_filename | string | none | picture file ame |
The "[cel]" section has the following possible parameters:
| parameter name | possible values | default values | note |
| src_filename | string | none | data file name |
| pic_filename | string | none | picture file ame |
The "[data]" section has the following possible parameters:
| parameter name | possible values | default values | note |
| src_filename | string | none | data file name |
| pic_filename | string | none | picture file ame |
Anyone can use the source codes, documents or the excutable file of CisGenome Browser free of charge for non-commercial use. For commercial use, please contact the author.
Jiang, H., Wang, F., Dyer, N.P., Wong, W.H. (2010)
CisGenome Browser: A Flexible Tool For Genomic Data Visualization
Bioinformatics, in press. [online]
CisGenome Browser was developed and tested with the help of the members and several collaborators of the Wong lab.