Encode Project Bigwig File Convention

Question

[Eric Ho]

(Maybe a stupid question.)

What is the file convention of bigWig file in ENCODE Project?
I could not find any clues from the ENCODE...

zero-based / one-based
and
half-open / fully-closed

Thanks!

[Neilfws]

Please define "file convention". Are you talking about 0/1-based start coordinates?

[Eric Ho]

Re Neilfws: Yes, you are right.

Answer 1

[Alex Reynolds]

Because bigWig is binary, you perhaps do not need to worry about its internal indexing. However, when converted back to something human-readable, like bed (0-based, half-open) or wig (1-based, closed), you might rely on that format's particular indexing scheme.

This is not a stupid question, by the way. Indexing is important to get right in bioinformatics (and in general applications of computer science).

[Eric Ho]

Thanks for you help. Your answer also solve my another question on bed and wig format convention.

Answer 2

[Eric Ho]

I have looked the BigWig paper, the supplement data shows that the BigWig stores chromStart and chromEnd as followings (Supplemental Table 13):

1. chromStart: Start position (starting with 0).
2. chromEnd: End of item. Same as chromStart + itemSize in bases.

Therefore, it should be 0-based and half-open.