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Section

The default output formad is BED, which describes the genomic region of the readBED 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 into in the poly-A tail are truncated to their respective content of genomic sequence. Reads In contrast, reads that fall completely into the poly-A tail and that are sequenced receive poly-A as a special sequence name in the generated BED file. The tag name is composed according to the description of the FMRD (Flux Mapped Read Descriptor) convention. Obviously, multi-map information is not provided and has to be obtained by a subsequent alignment of the reads. If the genomic sequence is provided, additionally FASTA/FASTQ sequences can be produced (see sequencing error models). The corresponding tag equals the BED name field plus the additional information about the genomic alignment, i.e., field 1,2,3,6,11 and 12 of the BED format.

 

Examples:
Here an example for a BED line that represents a spliced read

 

are described to be located on the special reference sequence 'poly-A'. The 12 tab-separated fields specified for the BED format are:

NrNameTypeDescription
1chromStringThe name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2chromStartIntegerThe starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3chromEndIntegerThe ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
4nameStringDefines 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.
5scoreIntegerUnused, set to '0'
6strand[+\-]The absolute directionality of the read; '+' denotes the same directionality as the reference sequende, '-' denotes that the read sequence is a reverse-complement of the reference sequence.
7thickStartIntegerUnused, set to '.'
8thickEndIntegerUnused, set to '.'
9itemRgb[0-9]+,[0-9]+,[0-9]+Unused, set to '0,0,0'
10blockCountIntegerNumber of alignment blocks for the read. Usually 1, but 2 or more in the case of reads that split-map.
11blockSizescomma-separated listA comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
12blockStartscomma-separated listA comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.


Example 

chr1 2082 2503 chr1:

...

4847775-4887990W:NM_001159750:1:

...

2668:

...

917:

...

1137:S/2 0 - 0 0 0,0,0 2 8,28 0,393


Section

In this example, the

The complete region of the read spans from 2083 (note the 0-base in BED in BED format) to position 2503 (which is the first excluded position in BED format and in BED format and therefore directly translates to the last included position in a 1-based coordinate system) on the reference sequence chr1. The the read alignment is split in two parts, one from 2083 to 2083+8-1=2090, and the other one from 2083+393=2476 to 2476+28-1=2502. The name 4th field denotes that the read has been the downstream mate P2 of a read pair, derived from the 105th transcript copy of the annotated uc009vip.1 structure (which has spliced length 2772) in splicing locus chr1:1116-4272W. The fragment of this transcript that has been sequenced starts at position 695 and ends at position 1003 in the spliced sequence, relative to the annotated transcription start. From this fragment, the subarea 968-1003 relative to the annotated transcription start has generated the readencodes the read ID, more information about Flux Simulator read identifiers can be found in the Sequencing Section.