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Old 09-18-2009, 02:16 PM   #13
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by Chipper View Post
Nils, do you have any results showing this or are you just guessing? If you have one end derived from an Alu repeat you would ve comparing it to ~1 M copies for singel end and perhaps 2-3 for paired ends with a 1 kb variabity so you should be able to find many more uniqe reads with paired ends.
The data on which I am basing my results is from actually trying this strategy in a version of my own mapping tool BFAST. The discordance between my results and your expectation may come from the sensitive settings I use for mappings (up to 10% raw error). I am always open to incorporating this strategy as it is trivial to implement. Nonetheless, I have myself neither performed nor seen how this strategy increases false-mappings for those cases when this strategy is used (I assessed only sensitivity).

This might actually be a good time to rigorously put this debate to rest with some simulations. What if I create some paired end data (from Human) with error-rates coming from our latest Illumina runs and check the false-mapping rates if this strategy is used? I can take those reads for which one end does not map and see how many I can recover, assessing both the sensitivity and false mapping rates. What do you think?
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