Difference Between Rr Ff And Rf Reads

Question

[Angel]

Hi:

I am wondering which fusion should I prioritize from a couple of candidates.

As you know tophat fusion generates a list with the direction of fusion mentioned as well. I am not a biologist and am wondering should I use directionality to prioritize one vs another to investigate further. E.g. are "rf" or "fr" be higher priority compared to "rr" or "ff".

Any suggestions, reference and biological insights will be greatly useful.

Thanks a ton!

[Pierre Lindenbaum]

cross posted on SE: http://seqanswers.com/forums/showthread.php?t=35289

Answer 1

[Devon Ryan]

I wouldn't recommend prioritizing followup by read-pair orientation. What I would recommend doing is prioritizing things by abundance of evidence. Having just one or two pairs with discordant orientations in a gene (or between genes) isn't as interesting as having 100 reads supporting a fusion/rearrangement (particularly if you have a couple reads indicating the break/fusion point). I would further prioritize candidates by biological relevance, if the fusion events accompany a phenotype of some sort (this may be a non-starter if you don't have much of a background in biology).