How to fix mix-orientation reads

[thermokarst]

@mimisikai

wonder QIMME2 must handle sequence with multiplexed reads?

In general, no - but in this case, if you had multiplexed reads, you could use the new mixed-orientation demux in q2-cutadapt 2020.6.

@mimisikai

I’m pretty sure I saw a thread in the forum said R1+R2 --> new R1, and R2+ R1 --> new R2, then somehow input newR1 and new R2 into Q2 for processing should be fix out this problem. I try to find this post but I cannot.

If you can get the multiplexed reads (or somehow make them by concatenating reads together), you could use q2-cutadapt.