Import of reverse reads

[SoilRotifer (Mike Robeson)]

Hi @Mandy,

Seems like you are on the right track given the following trick:

Miseq paired-end workflow

Hi @wym199633, I suspect that you should be able to trick QIIME 2 to import the reverse reads as forward reads by using the manifest format approach. That is, just set the direction column for these reads to forward for all your R2 reads, and do not include your R1 reads. I can not speak to any sequence data validation steps that occur via this or other import approaches. Perhaps @ebolyen, @thermokarst, or someone else can provide some insight on weather this will work, or if there is a more a…

But not the warning about naming:

Miseq paired-end workflow

Hi @wym199633, @SoilRotifer is correct — you can trick QIIME2 into using the reverse reads as forward reads by using the manifest file format. With the exception of the CASAVA1.8 paired-end format, which expects specific filename patterns to differentiate the forward and reverse reads, all other formats in QIIME2 are direction-agnostic.

-Mike