BED format

The BED (Browser Extensible Data) format has been developed by UCSC for displaying transcript structures in the genome browser, a full description of the format can be found there.

The following fields used by the Flux Capacitor and the Flux Simulator.

field Number description
1 chrom: the name of the chromosome or scaffold
2 chromStart: start position, first included position, in chromosomal coordinates 0-based
3 chromEnd: end position, first excluded position, in chromosomal coordinates 0-based
4 name read identifier in FMRD format
6 strand the genome strand the read aligns to
10 blockCount number of blocks, for spliced reads which are subdivided in blocks
11 blockSizes extension of each block, comma-separated list
12 blockStarts start of each block, relative to chromStart, 0-based

Note: The sanity check, $chromStart + blockStarts_k + blockSizes_k = chromEnd$ must always hold, for $k$ being the last (respectively, the unique) element in the block vector!

Examples

chr1    1723    1759    chr1:1116-4272W#uc009vip.1#45:234|P1    0    +    0    0    0,0,0    1    36    0
chr1    1921    1957    chr1:1116-4272W#uc009vip.1#45:234|P2    0    -    0    0    0,0,0    1    36    0
chr1    2062    2483    chr1:1116-4272W#uc009vip.1#46:216|P1    0    +    0    0    0,0,0    2    28,8    0,413
chr1    2627    2663    chr1:1116-4272W#uc009vip.1#46:216|P2    0    -    0    0    0,0,0    1    36    0
chr1    856324    861042    chr1:850393-869824W#uc001abw.1#2:224|P1    0    +    0    0    0,0,0    2    8,28    0,4690
chr1    864337    864518    chr1:850393-869824W#uc001abw.1#2:224|P2    0    -    0    0    0,0,0    2    35,1    0,180
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