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Old 12-22-2016, 04:51 AM   #7
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Location: Germany

Join Date: Apr 2012
Posts: 215

Originally Posted by Brian Bushnell View Post
Yes, to be honest, this does sound strange. Normally, contamination comes from 1 or 2 sources... a grab-bag of taxa is very unusual. Are you getting 100% identity to anything, or just weak hits?
And in addition: Do you get your complete read seq aligned or are your hits rather the tiny 20-40bp local alignment crap Blast may output if there is nothing more suitable?

EDIT: Just saw that you used Blastn. I'd suggest megablast here.

Last edited by WhatsOEver; 12-22-2016 at 04:54 AM.
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