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Old 06-09-2014, 12:27 PM   #1
haiwan
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Location: Sweden

Join Date: Nov 2013
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Default sequencing results generated by 16s-amplicon MiSeq

hi,

i am working on the bacterial community related to human disease by using 16s-based MiSeq. Recently, i have got the sequencing data which is aiming to optimize the 16s amplicon library in order to increase the Number of OTUs.
The results look like quite strange. 1) For example, there are many reads in one sample by contrast very few reads in the same sample (which means in duplicate). 2) Very few reads (4 reads) were generated by a number of copy number of input library (3,287,980 copy number of 16s detected by qPCR).
3) An important thing is nonmatched reads by index. There are 268,230 reads undetermined by index. This is a big headache. I didn't understand what happened there.
Could you please kindly explain the reasons for these above issues?

thank you very much indeed
kindly \haiw
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