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Old 11-29-2013, 09:23 AM   #1
Junior Member
Location: Washington

Join Date: Nov 2013
Posts: 1
Default high percentage of unclassified sequences on Illumina

Hi all,
I'm sequencing V6 region of bacterial 16S on an Illumina MiSeq and when I got my sequences back and process them using mothur, I'm getting a LOT of unidentified sequences. Like maybe 50% for some samples in the run. This wasn't the case for other Illumina runs on similar samples. Any ideas on what the cause may be? Is it appropriate to just remove these unidentified sequences from further analysis and publication or not? Your help is greatly appreciated.
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