How to handle mixed orientation reads

[ucassee]

Thanks for your help!
I am processing another pair-end sequences with single barcode. But I find if I use qiime1 (extract_barcodes.py ) to extract barcode.fq file , I will lose nearly half of my reads after demultiplexing. I think the reason is only half of my forward reads have the barcode in the begining while half of reversed reads have the barcode in the begining. Could you please give me some suggestions to deal with it?

[colinbrislawn (Colin J Brislawn)]

Hello @ucassee,

This is a great question, and I’m not sure there is an official solution. But have to try because we don’t want to lose have the reads!

I had a great discussion about this exact issue, and we discussed the options and what to try first. Let me know if you find this thread helpful: Dealing with non-oriented amplicon libraries

Let me know if you are able to try any of the suggestions in that thread, especially close-ref OTU picking.

Colin