I am reading the specifications of many range formats: BED, bigBED, bedGraph, Wig and BigWig. I am having a hard time summarizing which of these can store data that is either variableStep or fixedStep.
For each format, there is an important parameter/characteristic to understand:
- Size of the windows
- Space between the windows
With this in mind, range formats can be:
- fixedStep: This is when the data has values for :
- For every base OR
- For windows that are:
- regularly spaced
- variableStep: This is when the data has values for windows that are both:
- fixed sized
- variably spaced
With this in mind, is the following correct?
BED: accommodates arbitrarily sized ranges
“The span specification in wiggle formats has a very specific use and is not to be used to specify arbitrarily sized data items (that's what the BED format is for)”
Additionally, the bigBED specification link says: “The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as bed files do.” - suggesting that BED files can do variableStep at least.
=> Sounds like BED is the most simple format that can story range that be arbitrarily sized.
BigBED: idem as BED since it's made from a BED file
bedGraph: it accommodates windows that are both variably sized and variablly spaced (sort variableStep but not fixed-sized windows)
WIG: it accommodates either fixedStep or variableStep
bigWig: idem as WIG OR idem as bedGraph, depending on how it was made
Sorry if the question is basic but with all these similar formats, I am finding it hard to be sure and I find the distinction between size and space between windows confusing. And I feel it's important to understand the difference if I am to choose the right format.