I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C to T changes than G to A changes, when it would be expected that these numbers would be relatively the same.

So, in vivo when a C to T transition occurs, does the complementary base get changed to ensure watson and crick binding, or will you end up with a T-G pair? This would explain the phenomenon that I am seeing but I don't know if this happens. (Andy references would also be super helpful. Thanks.)

  • $\begingroup$ Depending on how your sequencing data is being presented to you, this may not be an issue. Are you looking at FASTQs, BAMs, VCFs? In my experience (human resequencing), variants are generally reported from one strand instead of both -- that is, a variant, which really causes two paired bases to change in tandem, is represented in the results by just a single letter change. When a C to T transition occurs, I would assume it's a C-G pair transitioning to a T-A pair, unless your biological or sequencing situation is unusual somehow. Give us a bit more detail about your file format and sequencer. $\endgroup$ – Jenn D. Aug 6 '16 at 1:03
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    $\begingroup$ You have not told us what kind of sequencing data you are using, for example in bisulfite sequencing you change non-methylated C to U which are read as T. The context is very important here. $\endgroup$ – FoldedChromatin Aug 8 '16 at 7:42
  • $\begingroup$ @KoustavPal This is deep genome sequencing from an Illumina 4000. $\endgroup$ – The Nightman Aug 9 '16 at 16:12

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