When in this format, the assumption is that the coordinates are 0-start, half-open.Spaces between chromosome, start coordinate, and end coordinate.
![different file formats for ucsc genome browser different file formats for ucsc genome browser](http://homer.ucsd.edu/homer/basicTutorial/UCSCsettings.png)
The “BED” format (referring to the “0-start, half-open” system) When in this format, the assumption is that the coordinate is 1-start, fully-closed.Includes punctuation: a colon after the chromosome, and a dash between the start and end coordinates.The “Position” format (referring to the “1-start, fully-closed” system as coordinates are “positioned” in the browser) The UCSC Genome Browser and many of its related command-line utilities distinguish two types of formatted coordinates and make assumptions of each type. Section 3: Formatting Coordinate formatting indicates interval type This figure describes the differences in defining and calculating the range for a specified sequence highlighted in yellow, “T, C, G, A.”įigure 4. (To enlarge, click image.) Calculation of genomic range for comparing “1-start, fully-closed” vs. We calculate that we have 5 digits because 5 (range end after pinky finger) – 0 (the thumb, range start) = 5.Īnother example which compares 0-start and 1-start systems is seen below, in Figure 4. 0-start, hybrid-interval (interval type is: start-included, end-excluded)įigure 3. (To enlarge, click image.) The UCSC Genome Browser coordinate system for databases/tables (not the web interface) is “0-start, half-open” where start is included (closed-interval), and stop is excluded (open-interval).A “1-based end” refers to the end of the range being included, as in the common “1-based, fully-closed” system. Note: This is not technically accurate, but conceptually helpful.To increase efficiency, the UCSC Genome Browser uses a “hybrid-interval” coordinate system for storing coordinates in databases/tables that is referred to as “0-start, half-open” (see Figure 3, below).Īlthough coordinates in the web browser are converted to the more human-readable “1-start, fully-closed” system, coordinates are stored in database tables as “0-start, half-open.” You may have heard various terms to express this 0-start system: While the commonly-used “one-start, fully-closed” system is more intuitive, it is not always the most efficient method for performing calculations in bioinformatic systems, because an additional step is required to calculate the size of the base-pair (bp) range. UCSC Genome Browser tables = “0-start, half-open” We then need to add one to calculate the correct range 4+1= 5. We calculate that we have 5 digits because 5 (pinky finger, range end) – 1 (the thumb, range start) = 4. Used within the UCSC Genome Browser web interface (but not used in UCSC Genome Browser databases/tables). (To enlarge, click image.) 1-start, fully-closed interval. However, all positional data that are stored in database tables use a different system.įigure 2. The “1-start, fully-closed” system is what you SEE when using the UCSC Genome Browser web interface. Note that an extra step is needed to calculate the range total (5). UCSC Genome Browser web interface = “1-start, fully-closed”Ī common counting convention is a system that we all used when we first learned to count the fingers on our hands this is referred to as the “one-based, fully-closed” system ( Figure 2, below). Section 2: Interval types in the UCSC Genome Browser
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Figure 1 below describes various interval types.įigure 1. (To enlarge, click image.) Description of interval types. For further explanation, see the interval math terminology wiki article. You might recall that specifying an interval type as open, closed (or a combination, e.g., “half-open”) refers to whether or not the endpoints of the interval are included in the set. Sometimes referred to as “0-based” vs “1-based” or “0-relative vs “1-relative.”įor a counted range, is the specified interval fully-open, fully-closed, or a hybrid-interval (e.g., half-open) ? Positioned in UCSC Genome Browser web interfaceĠ-start vs. When using “position” format, browser & utilities When using BED format, browser & utilities UCSC Genome Browser coordinate systems summary “0-start, half-open” = coordinates stored in database tables. “1-start, fully-closed” = coordinates positioned within the web-based UCSC Genome Browser.