What is the required format for a BED file defining a kit?
As part of the management settings (30.0+), 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:
Chromosome - The name of the chromosome has to be sorted in alpha-numeric order. example: chr1, chr2, ..., chr12, ..., chr22, chrX, chrY, chrM.
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.
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.
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.
Last updated
Was this helpful?