Required format for a BED file defining a kit

As part of the management settings, users can upload BED files to be associated with their kits.

The format of the BED file (.bed) is following the description from UCSC Genome Browser with some modifications:

• The file has to be a tab-delimited text file;

• The file should not contain headers;

• The number of fields per line must be consistent throughout any single set of data.

• Zero-based index: Start and end positions are identified using a zero-based index.

There are three required fields:

1. Chromosome - The name of the chromosome has to be sorted in alpha-numeric order. example: chr1, chr2, ..., chr12, ..., chr22, chrX, chrY, chrM.

2. Chromosome Start - The starting position of the feature in the chromosome. The start position has to be smaller than the end position. The data has to be sorted in numeric order.

3. Chromosome End - The ending position of the feature in the chromosome. The end position has to be greater than the start position. The data has to be sorted in numeric order.

To add a region name to a BED file, include it as an additional column. This name will be displayed in place of the actual region location for insufficient regions, making it easier to review these areas on the Lab page.

Example:

chr1	40794900	42795220  
chr1	75796785	76799036  
chr2	21224573	21226251  
chr2	51227067	61227587  
chr3	10183418	10184013  
chr3	141327248	141327582  
chr5	33944704	33945028  
chr5	112173191	112179935  
chr6	31973380	31973922  
chr6	118880009	118880306  
chr10	43572669	43572871  
chr10	43595829	43596269  
chr11	532524	532797  
chr11	108225486	108225731  
chr20	10620075	10620661  
chr20	43058101	43058438  
chr21	35742663	35743177  
chr21	35821512	35822069  
chr22	21336576	21336967  
chr22	29133150	29133387  
chrX	9693690	9693958  
chrX	153599135	153599723  
chrY	2654931	2655693  
chrM	108	596

Newly uploaded BED files will become available for use only after a mandatory waiting period of one hour to ensure adequate time for synchronization to complete.