【3D Genome】 BEDPE the format of chromatin looping

BEDPE (.bedpe) was a format extended from BED format for 2 dimension information. Because the BED format was designed for 1 dimension feature such as ChIP-Seq data which could not represent two loci for a single data point, BEDPE was introduced and was supported by massive data analysis tools in recent days and has become a standard. Especially in representing chromosome looping the common format is BEDPE8 and BEDPE10. When we used hichipper to analyze HiChIP data, the output of loops was stored in BEDPE8 format.

For example:

chr1  10   20   chr5  50  51  .  2

The fields in order are:

chr_A / start_A / end_A / chr_B / start_B / end_B / record_name / score / strand_A / strand_B

1. A's chromosome number
2. A's start position
3. A's end position
4. B's chromosome number
5. B's start position
6. B's end position
7. The name of this data point (if Null can fill with a dot "." )
8. Intensity of this data point.
9. A`strand(transcription direction)
10. B`strand(transcription direction)

For the chromatin loop (looping), A and B are the two anchor points of the loop (loop anchors). Those two positions are also where the chromatin loop starts and ends.

References:

https://bedtools.readthedocs.io/en/latest/content/general-usage.html
https://github.com/YaqiangCao/cLoops/blob/master/scripts/hicpropairs2bedpe

Ming Han Yang

A passionate bioinformatician focuses on the next generation of medical science and biotechnology.

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