Gigabase Clarification (Same as Gigobyte?)

Question

[joe_genome]

Hello,

So I'm a bit confused on how the terms gigabase (Gb) and gigabyte (GB) overlap or better said, differ. I am trying to determine the amount of current disk space I have available and how to calculate how many gigabases are determined per bases per fastq file.

For example:

Let's say I have 250000GB available and have already processed 215118590880 bases, thus implies 0.1% of my space has been used I can say, or would this be the equivalent of 0.1% of gigabases and not gigobytes?

Thank you in advanced!

[lieven.sterck]

well for sure gigabase is not equal to gigabyte. first one is just 1000M bases, the later one is a measure of disk capacity for storing data. converting the two will depend on the encoding used I assume

Answer 1

[Carambakaracho]

With regular UTF-8 encoding it is safe to assume 1 base character translates to 1 byte. However, you have to add overhead storage for the filetypes and of course, sequence headers and quality strings (for example, which double the number of characters per base).

Often sequences are stored as compressed archives, where the required storage depends archive type and the complexity of the character strings in a relation that beats me. As far as I remember, I never observed compression rates higher than 20%.

[joe_genome]

Perfect, thanks for the clarification on this in such a detailed mannar. I appreciate it quite a lot, definitely points me in the right direction. Cheers