BED (file format)
|Internet media type|
|Type of format||Text file|
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project and then adopted by other sequencing projects. As a result of this increasingly wide use, this format has become a de facto standard in bioinformatics without receiving any official specifications.
One of the advantages of this format is the manipulation of coordinates instead of nucleotide sequences, which optimizes the power and computation time when comparing all or part of genomes. In addition, its simplicity makes it easy to manipulate and read (or parsing) coordinates or annotations using word processing and scripting languages such as Python, Ruby or Perl or more specialized tools such as BEDTools.
The end of the 20th century saw the emergence of the first projects to sequence complete genomes. Among these projects, the Human Genome Project was the most ambitious at the time, aiming to sequence for the first time a genome of several gigabases. This required the sequencing centres to carry out major methodological development in order to automate the processing of sequences and their analyses. Thus, many formats were created, such as FASTQ, GFF or BED. However, no official specifications were published, which affected some formats such as FASTQ when sequencing projects multiplied at the beginning of the 21st century.
Its wide use within genome browsers has made it possible to define this format in a relatively stable way as this description is used by many tools.
A BED file consists of a minimum of three columns to which nine optional columns can be added for a total of twelve columns. The first three columns contain the names of chromosomes or scaffolds, the start, and the end coordinates of the sequences considered. The next nine columns contain annotations related to these sequences. These columns must be separated by spaces or tabs, the latter being recommended for reasons of compatibility between programs. Each row of a file must have the same number of columns. The order of the columns must be respected: if columns of high numbers are used, the columns of intermediate numbers must be filled in.
|1||chrom||Chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671) name|
|2||chromStart||Start coordinate on the chromosome or scaffold for the sequence considered (the first base on the chromosome is numbered 0)|
|3||chromEnd||End coordinate on the chromosome or scaffold for the sequence considered. This position is non-inclusive, unlike chromStart.|
|4||name||Name of the line in the BED file|
|5||score||Score between 0 and 1000|
|6||strand||DNA strand orientation (positive ["+"] or negative ["-"] or "." if no strand)|
|7||thickStart||Starting coordinate from which the annotation is displayed in a thicker way on a graphical representation (e.g.: the start codon of a gene)|
|8||thickEnd||End coordinates from which the annotation is no longer displayed in a thicker way on a graphical representation (e.g.: the stop codon of a gene)|
|9||itemRgb||RGB value in the form R,G,B (e.g. 255,0,0) determining the display color of the annotation contained in the BED file|
|10||blockCount||Number of blocks (e.g. exons) on the line of the BED file|
|11||blockSizes||List of values separated by commas corresponding to the size of the blocks (the number of values must correspond to that of the "blockCount")|
|12||blockStarts||List of values separated by commas corresponding to the starting coordinates of the blocks, coordinates calculated relative to those present in the chromStart column (the number of values must correspond to that of the "blockCount")|
A BED file can optionally contain a header. However, there is no official description of the format of the header. It may contain one or more lines and be signified by different words or symbols, depending on its functional role or simply descriptive. Thus, a header line can begin with these words or symbol:
- "browser": functional header used by the UCSC Genome Browser to set options related to it,
- "track": functional header used by genome browsers to specify display options related to it,
- "#": descriptive header to add comments such as the name of each column.
Unlike the coordinate system used by other standards such as GFF, the system used by the BED format is zero-based for the coordinate start and one-based for the coordinate end. Thus, the nucleotide with the coordinate 1 in a genome will have a value of 0 in column 2 and a value of 1 in column 3.
A thousand-base BED interval with the following start and end:
chr7 0 1000
would convert to the following 1-based "human" genome coordinates, as used by a genome browser such as UCSC:
chr7 1 1000
This choice is justified by the method of calculating the lengths of the genomic regions considered, this calculation being based on the simple subtraction of the end coordinates (column 3) by those of the start (column 2): . When the coordinate system is based on the use of 1 to designate the first position, the calculation becomes slightly more complex: . This slight difference can have a relatively large impact in terms of computation time when data sets with several thousand to hundreds of thousands of lines are used.
Alternatively, we can view both coordinates as zero-based, where the end position is non-inclusive. In other words, the zero-based end position denotes the index of the first position after the feature. For the example above, the zero-based end position of 1000 marks the first position after the feature including positions 0 through 999.
Here is a minimal example:
chr7 127471196 127472363 chr7 127472363 127473530 chr7 127473530 127474697
Here is a typical example with nine columns from the UCSC Genome Browser. The first three lines are settings for the UCSC Genome Browser and are unrelated to the data specified in BED format:
browser position chr7:127471196-127495720 browser hide all track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On" chr7 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0 chr7 127472363 127473530 Pos2 0 + 127472363 127473530 255,0,0 chr7 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0 chr7 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0 chr7 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255 chr7 127477031 127478198 Neg2 0 - 127477031 127478198 0,0,255 chr7 127478198 127479365 Neg3 0 - 127478198 127479365 0,0,255 chr7 127479365 127480532 Pos5 0 + 127479365 127480532 255,0,0 chr7 127480532 127481699 Neg4 0 - 127480532 127481699 0,0,255
There is currently no standard file extension for BED files, but the ".bed" extension is the most frequently used. The number of columns sometimes is noted in the file extension, for example: ".bed3", ".bed4", ".bed6", ".bed12".
The use of BED files has spread rapidly with the emergence of new sequencing techniques and the manipulation of larger and larger sequence files. The comparison of genomic sequences or even entire genomes by comparing the sequences themselves can quickly require significant computational resources and become time-consuming. Handling BED files makes this work more efficient by using coordinates to extract sequences of interest from sequencing sets or to directly compare and manipulate two sets of coordinates.
To perform these tasks, various programs can be used to manipulate BED files, including but not limited to the following:
- Genome browsers: from BED files allows the visualization and extraction of sequences of mammalian genomes currently sequenced (e.g. the function Manage Custom Tracks in UCSC Genome Browser).
- Galaxy : web-based platform.
- Command-line tools:
- BEDTools: program allowing the manipulation of coordinate sets and the extraction of sequences from a BED file.
- BEDOPS: a suite of tools for fast boolean operations on BED files.
- BedTk: a faster alternative to BEDTools for a limited and specialized sub-set of operations.
- covtobed: a tool to convert a BAM file into a BED coverage track.
BEDtools also uses .genome files to determine chromosomal boundaries and ensure that padding operations do not extend past chromosome boundaries. Genome files are formatted as shown below, a two-column tab-separated file with one-line header.
chrom size chr1 248956422 chr2 242193529 chr3 198295559 chr4 190214555 chr5 181538259 chr6 170805979 chr7 159345973 ...
- Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM. & Haussler D. (2002). "The human genome browser at UCSC". Genome Research. 12 (6): 996–1006. doi:10.1101/gr.229102. ISSN 1088-9051. PMC 186604. PMID 12045153.CS1 maint: multiple names: authors list (link)
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- "Frequently Asked Questions: Data File Formats. BED format". UCSC Genome Browser. University of California Santa Cruz Genomics Institute. Retrieved 2 October 2019.
- Quinlan, AR; Hall, IM (21 September 2010). The BEDTools manual (PDF). Retrieved 3 October 2019.
- "Datatypes". Galaxy Community Hub. Retrieved 3 October 2019.
- Neph, S; Kuehn, MS; Reynolds, AP; Haugen, E; Thurman, RE; Johnson, AK; Rynes, E; Maurano, MT; Vierstra, J; Thomas, S; Sandstrom, R; Humbert, R; Stamatoyannopoulos, JA (15 July 2012). "BEDOPS: high-performance genomic feature operations". Bioinformatics. 28 (14): 1919–20. doi:10.1093/bioinformatics/bts277. PMC 3389768. PMID 22576172.
- Li, Heng. "BedTk". GitHub. Retrieved 22 July 2020.
- Birolo, Giovanni; Telatin, Andrea (6 March 2020). "covtobed: a simple and fast tool to extract coverage tracks from BAM files". Journal of Open Source Software. 5 (47): 2119. Bibcode:2020JOSS....5.2119B. doi:10.21105/joss.02119.