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Old 11-10-2009, 10:24 AM   #2
amcrisan
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Location: Canada

Join Date: Oct 2009
Posts: 9
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That's difficult to say. The -m unique option will avoid giving you all the possible reads like the -m all option. However, all it does (according to the documentation) is really set aside any reads which can map to multiple locations, it doesn't take the highest scoring alignment out of all the possible alignment locations for that read. Additionally I don't see any indication that it actually would.

The best you can do in my opinion is to use the -m unique option, and then later you can use MosaikSort and tell it to try resolve multiple vs multiple (-rmm) read pairs, and so on. That being said, you may still get things discarded, as it may not be possible to resolve the multiple vs. multiple.

Lastly, using the -m unique option is faster and takes less space. You could also use the -m all option followed by MosaikSort for I think similar outcomes to using the unique option (not 100% sure though..).

Hope that's helpful.
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