What Does Color Space And Nucleotide Space Mean (Data, Reference Genome Etc.) ?

Question

[Sukhi Singh]

Hi guys,

I am not sure, in terms of sequencing what is referred to as color space and nucleotide space. What is a difference between a normal reference genome and a color space genome. Does it has to do something with base calling, that the original data is retained without the conversions to textual nucleotide data!!!! What we use in normal chip-seq and rna-seq analysis.

There's a kind of similar question here but the answer is missing the link.

Thanks

Answer 1

[swbarnes2]

Short answer: color space refers to the native format of ABI SoLID technology. Color space is translated to nucleotide, or base space (same thing) so that it can be understood.

That technology is not growing in market share, so in the next few years it will become less common. ABI is putting most of their effort behind the Ion Torrent now.

Answer 2

[Istvan Albert]

Here is a tutorial I wrote on this topic:

• Transforming And Manipulating Color Space Reads

Answer 3

[Giovanni M Dall'Olio]

Apart from the excellent tutorial by Albert, I recommend you to read this blog post on Color Space sequencing: http://www.homolog.us/blogs/2010/02/15/the-mathematics-behind-color-space-sequencing/

Answer 4

[Leonor Palmeira]

It is also useful to re-read the details regarding the SOLID platform, and the dealing of errors in color-space, provided on SEQAnswers: http://seqanswers.com/forums/showthread.php?t=10