encode project .bb annotation files

Question

[janeshen91]

I've been looking at ENCODE's annotation files such as the one below

https://www.encodeproject.org/documents/46933bb0-e974-4976-87e9-aa671046d106/@@download/attachment/ENCODEElementsprototypeREADME.pdf

It seems to be a good resource, as it combines multiple types of data (chipseq, DNase HS) across multiple cell lines to generate annotations such as enhancers and transcription factor binding. However, the files are all in .bb form. I'm not sure what kind of file it is? When I've downloaded one the beginning of the file looks like this:

"BED9+ with additional details about peaks merged"

(
string chrom;      "Reference sequence chromosome or scaffold"
uint   chromStart; "Start position in chromosome"
uint   chromEnd;   "End position in chromosome"
string name;       "Short Name of item"
uint   score;      "Score from 0-1000"
char[1] strand;    "+ or -"
uint thickStart;   "Start of where display should be thick (start codon)"
uint thickEnd;     "End of where display should be thick (stop codon)"
uint reserved;     "Used as itemRgb as of 2004-11-22"
float details;   "Percentile of H3K27ac signal over background distribution"
)

which leads me to expect a bed file, however it is a binary files. Does anyone have any suggestions as to how to open it/extract the contents?

Thank you

Answer 1

[PoGibas]

Yes, this is bed file and it's binary :-) bb files are bigBed (on UCSC there is good description about bigBed files also how to convert them to bed).