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Encode Project Bigwig File Convention

(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!

bigwig

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

Re Neilfws: Yes, you are right.

2 answers

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).

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

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.

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