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
