Sequence Tube Map Usage Guide
The Sequence Tube Map is used to generate visualizations of genomic sequence graphs. This guide will demonstrate how to select custom data to visualize. You can also read this guide on Github.
Selecting Tracks
The following procedure describes adding and updating settings of custom tracks. You can use a custom track to load your own graph file, haplotype database, or file of aligned reads.
- From the "Data" dropdown box, select "custom (mounted files)"
- Select the button that says "Configure Tracks".
- Once the button is clicked on, a popup with a "+" button will be displayed. Click on this button to add tracks.
- Select a graph, read, or haplotype track from the first dropdown. Make sure to always have at least 1 graph track. Select a data file from the list of files of that type in the second dropdown.
- Click on the settings button, where there are options to color the tracks from an existing color palette, or select any other color.
- To delete a track, click on the button with the "x" icon.
Displaying Visualizations
- Add as many tracks as needed and exit the track picker.
- Add a BED file, if needed. This step is optional.
- Specify a region input. The region input can be:
- A coordinate range (e.g. "chr1:1-100")
- A node ID range (e.g. "node:100-110")
- A start position and a distance (e.g. "chr1:1+100")
- A node ID anchor and a distance (e.g. "node:100+10")
- If simplifying the BED file chunk or graph is possible, users will see a "Simplify Off" button, which when clicked with toggle to "Simplify On". This option enables vg simplify, which would remove small snarls. This option will only appear when there aren't any reads to be displayed.
- Click Go to see the selected tracks render in the visualization area.
How to make link-to-view URLs
Users can compose URLs that link to a specific view, or a visualization of genomic data. The link describes which tracks and files will be displayed.
Query String Encoding
The link has a query string that consists of key-value pairs separated by ampersands, where the keys are not URL-econded and the values are URL-encoded.
Keys can use brackets to encode hierarchical structures such as arrays and objects.
- For arrays, put a number in brackets to assign a new value to or access a value in that entry in the array.
- For objects, put the key's name in brackets to assign a new value to or access a value in that entry in the object.
The key's name should not be in quotes.
Example of an array of JSON objects:
object =
[
{
"a": "b",
},
{
"c": "d",
"e": {
"f": "g"
}
},
]
This array's query string representation would be: object[0][a]=b&object[1][c]=d&object[e][f]=g.
Fields that can be included in the link URL:
-
tracksArray of tracks. Tracks are objects consisting of
trackFile,trackType, andtrackColorSettings.A track object in JSON format might look like this:
{ "trackFile": "exampleData/internal/snp1kg-BRCA1.vg.xg", "trackType": "graph", "trackColorSettings": { "mainPalette": "greys", "auxPalette": "ygreys", "colorReadsByMappingQuality": false } }The collection of tracks wil be encoded as query string parameters starting with tracks.
-
trackFile: the path (from the server working directory) or URL (any HTTP/HTTPS URL) to the track file.- Examples:
- File in server working directory:
tracks[0][trackFile]=exampleData/internal/snp1kg-BRCA1.vg.xg. - HTTP/HTTPS URL:
tracks[0][trackFile]=https://public.gi.ucsc.edu/~anovak/graphs/trivial-brca1.vg.
- File in server working directory:
- Examples:
-
trackType: the type of the track, which can begraph,haplotype,read.- Example:
tracks[0][trackType]=graph.
- Example:
-
trackColorSettings(optional): the color information for the track. It has subfields:-
mainPaletteandauxPalette(optional): The "main" and "auxilliary" color palettes to use, respectively. The values for each palette can be a hex code starting with a#, or one of the premade palette names:greys,ygreys,blues,reds,plainColors, orlightColors. - The palettes are used differently for different track types.
- Graphs: the
mainPalettecolors the primary reference path whileauxPaletteis used for the other paths. - Haplotypes: only the
mainPaletteis used. - Reads: the
mainPalettecolors the forward-strand reads and theauxPalettecolors the reverse-strand reads. - Examples:
-
tracks[0][trackColorSettings][mainPalette]=greys. -
tracks[0][trackColorSettings][auxPalette]=ygreys.
-
- Graphs: the
-
colorReadsByMappingQuality(optional) is a boolean value that determines if reads are colored based on their mapping quality or not. It defaults tofalse.- Example:
tracks[0][trackColorSettings][colorReadsByMappingQuality]=true.
- Example:
-
-
-
regionRegion coordinates. This region will be loaded in the Tube Map visualization once the link is followed. Syntax of region coordinates is documented at step 3 of Displaying Visualizations.
- Example:
region=17%3A1-100.
- Example:
-
bedFile(optional)A BED file containing coordinates for regions of interest, some of which may have associated pre-extracted Tube Map views. More information on BED file structure and creation is documented here.
- Examples:
- File in server working directory:
bedFile=exampleData/internal/snp1kg-BRCA1.bed. - HTTP/HTTPS URL:
bedFile=https://raw.githubusercontent.com/vgteam/sequenceTubeMap/ca4f2485231ee4182173bec19489ba940b27461a/exampleData/cactus.bed. - No BED file:
bedFile=none.
- File in server working directory:
- Examples:
-
dataTypeInformation about the type of data. Data can be
built-in,mounted files, or syntheticexamples.-
built-in: Predefined data sources from the server configuration file. If thedataTypefield is set tobuilt-in, you should set thenamefield to the name of a data source defined inDATA_SOURCESinconfig.json. -
mounted files: If thedataTypefield is set tomounted files, thenamefield must be set tocustom, and you should provide custom tracks along with an optionalbedFile. - Examples:
-
dataType=built-in. -
dataType=mounted%20files.
-
-
-
simplifyWhether small snarls (e.g. single base indels and SNPs) are displayed or removed. It defaults to false, which means that the small snarls are not removed. Currently, this option cannot be used if there are any read tracks.
- Example:
simplify=false.
- Example:
-
nameName of data. This is a field that indicates the name of preset data, which is defined in
DATA_SOURCESinconfig.json.nameis used whendataTypeis set tobuilt-in. You do not have to use these presets. IfdataTypeismounted files, this field should be set tocustom.- Examples:
-
name=snp1kg-BRCA1. -
name=custom.
-
- Examples:
Examples of links:
- Link with preexisting data:
http://127.0.0.1:3001? tracks[0][trackFile]=exampleData%2Finternal%2Fsnp1kg-BRCA1.vg.xg& tracks[0][trackType]=graph&tracks[0][trackColorSettings][mainPalette]=greys& tracks[0][trackColorSettings][auxPalette]=ygreys& tracks[1][trackFile]=exampleData%2Finternal%2FNA12878-BRCA1.sorted.gam& tracks[1][trackType]=read&bedFile=exampleData%2Finternal%2Fsnp1kg-BRCA1.bed& name=snp1kg-BRCA1& region=17%3A1000-1200& dataType=built-in& simplify=false - Link with custom data:
http://127.0.0.1:3001? tracks[1][trackType]=graph& tracks[1][trackColorSettings][mainPalette]=%23000000& tracks[1][trackColorSettings][auxPalette]=greys& tracks[1][trackColorSettings][colorReadsByMappingQuality]=false& tracks[1][trackFile]=exampleData%2Fcactus.vg& tracks[2][trackType]=read& tracks[2][trackColorSettings][mainPalette]=blues& tracks[2][trackColorSettings][auxPalette]=reds& tracks[2][trackColorSettings][colorReadsByMappingQuality]=false& tracks[2][trackFile]=exampleData%2Fcactus0_10.sorted.gam& bedFile=none& region=ref%3A2000-3000& dataType=mounted%20files& simplify=false
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
The newlines here get lost when the Markdown is rendered (see the rich diff). And among the various fields there are several different structures right after the number: field name and a noun phrase, field name and a sentence, field name and a verb phrase ("Describes ..."). So we probably should settle on one structure with a separator between the
fieldand the description. I would recommend using a colon and than an un-capitalized noun phrase with a "the", describing what goes in the field, and ending with a period, like this:foobar: the foo to bar. Now I can talk more about what the semantics of foos and bar-ing are in a few more sentences.foobar=this_foocatCount: the number of cats to be included in the request. No cats will be harmed while processing the request.catCount=2I like including the example as a nested bullet so I am showing that here too.
The important thing is to be consistent across all the fields. They should all, as far as possible, follow the same pattern.