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16s analysis MySeq PE - analysis of only forward reads?

Dear all, I have information from a company that 16s V3-V5 metagenomics data from MiSeq PE 2x300 and they analyze only the Forward reads from the sample (no joining the reads). I was wondering which approach can be more accurate - joining the reads and losing some reads or using only the forwards?

16s metagenomics
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updated by Asaf Asaf • written by manekineko manekineko

1 answer

If you loose reads when joining paired reads it means that they were problematic to start with, you only disregarded this information. I think you'll get more reliable and accurate results using the paired-end data

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written by Asaf Asaf

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