I am a student working on microbiota. I am using the V3-V4 hypervariable region 16S rRNA gene to target the bacteria. After merging the forward and reverse reads, I would want them to be globally trimmed so that the reads have the same length. Does QIIME2 really have this option? If not, does it matter (in the downstream analyses) if the merged reads are of variable lengths?
No. Though you could join reads with q2-vsearch, then denoise with q2-deblur, which has a truncation parameter that you can use to accomplish this. So yes, but only if you follow that path.
No, it should not. Your merged reads should theoretically be the full amplicons, so differing lengths represents “true” biological variation. Most downstream methods should be okay with different-length sequences, though I can’t guarantee that.
Makes great sense.
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