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Old 12-21-2016, 02:13 PM   #4
TomHarrop
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Location: New Zealand

Join Date: Jul 2014
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I blastn-ed 1000 R1 and 1000 R2 reads from this library against the 'nt' database. For R1, I got 544 hits with an evalue < 1. 493 of them had usable taxon identifiers. From that I got 89 plant hits (18%), 82 mammalian (17%), 65 insects (13%), 63 nematodes and 57 fish (and some other stuff). R2 numbers were similar.

I don't know if evalue is the best way to look at BLAST results for NGS reads (i.e. short queries), but either way it looks like contamination to me.

Thanks for the hint.

Last edited by TomHarrop; 01-10-2017 at 06:39 PM. Reason: more concise
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