View Single Post
Old 09-16-2009, 03:50 PM   #4
Nils Homer
nilshomer's Avatar
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Originally Posted by simonandrews View Post
It's certainly possible. Most paired end mapping algorithms are able to use mapping information about one end to infer a likely position for the other, meaning that a read which in isolation couldn't be mapped uniquely can be positioned if the position of its other end is known.

If you see a big difference in efficiency I'd also double check that you were using the same mapping parameters in both runs just to be sure. Using 75bp reads I'd be surprised if there was a big advantage to using paired end over single end mapping for a cDNA library.
I would argue that the strategy above shows a common misconception about paired end data (or mate-end). For the human genome, inferring one end from the other does not return much, due to the local nature of repeats (think of insert distributions that are >500bp wide and how local repeats would confound placing the unaligned end). I have seen no data to show what inferring one end from the other does to false mappings, especially around large-scale insertion, deletion, and translocation events. At my current state of thinking, using paired end constraints during mapping is a heuristic to make up for the fact you did not map each end sensitively enough.
nilshomer is offline   Reply With Quote