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The BED format is employed as default for describing reads produced in a= Flux Simulator run by the genomic regions from which they are originating.= Reads that fall partially in the poly-A tail are truncated to their respec= tive content of genomic sequence.In contrast, reads that fall completely in= to the poly-A tail are described to be located on the special reference seq= uence 'poly-A'. The 12 tab-separated fields specified for the BED format ar= e:
Nr | Name | Type | Description |
---|---|---|---|
1 | chrom | String | The name of the chromosome (e.g. chr3, chrY, chr= 2_random) or scaffold (e.g. scaffold10671). |
2 | chromStart | Integer | The starting position of the feature in the chro= mosome or scaffold. The first base in a chromosome is numbered 0. |
3 | chromEnd | Integer | The ending position of the feature in the chromo= some or scaffold. The chromEnd base is not included in the display= of the feature. For example, the first 100 bases of a chromosome are defin= ed as chromStart=3D0, chromEnd=3D100, and span the bases numbered = 0-99. |
4 | name | String | Defines the name of the BED line. This label is = displayed to the left of the BED line in the Genome Browser window when the= track is open to full display mode or directly to the left of the item in = pack mode. |
5 | score | Integer | Unused, set to '0' |
6 | strand | [+\-] | The absolute directionality of the read; '+' den= otes the same directionality as the reference sequende, '-' denotes that th= e read sequence is a reverse-complement of the reference sequence. |
7 | thickStart | Integer | Unused, set to '.' |
8 | thickEnd | Integer | Unused, set to '.' |
9 | itemRgb | [0-9]+,[0-9]+,[0-9]+ | Unused, set to '0,0,0' |
10 | blockCount | Integer | Number of alignment blocks for the read. Usually= 1, but 2 or more in the case of reads that split-map. |
11 | blockSizes | comma-separated list | A comma-separated list of the block sizes. The n= umber of items in this list should correspond to blockCount. |
12 | blockStarts | comma-separated list | A comma-separated list of block starts. All of t= he blockStart positions should be calculated relative to chrom= Start. The number of items in this list should correspond to block= Count. |
chr1 2082 2503 chr1:4847775-4887990W:NM_001159750:1:2668:917:113=
7:S/2 0 - 0 0 0,0,0 2 8,28 0,393
=
In this example, the complete region of th=
e read spans from