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Old 01-06-2009, 10:49 AM   #17
dvh
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Location: london, uk

Join Date: Jul 2008
Posts: 35
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Quote:
Originally Posted by bioinfosm View Post
Hi all,

Thanks for the technical details on this. Anyone got some information about bioinformatics on adapter contamination detection and removal. I tried using adapter sequences with eland to check for contamination, but less than 1% reads aligned. I expected more as less than 10% reads aligned to actual reference.

I know of a file one can specify in GA pipeline, to exclude sequences -- could someone point more details on the same? (i tried bioinformatics thread, but did not hear back )

thanks!
novoalign has 5' and 3' removal of adapter sequences prior to alignment. works well.
david
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