I used the following primers to analyze V3-V4 from mice fecal samples:
Unfortunately, there was an issue and we ended up sequencing PE150. For analysis using QIIME2, I took two approaches: 1) treat as single-end, and 2) for merge using DADA2 justConcatenate. After denoising, I loose a lot of sequences (on average, only 10% of entire sequence is recovered).
My questions are:
Is it okay to assume that such low recovery rate after denoising is due to short sequencing reads? (after trimming, a get 110bp reads)
My sequencing depth was 1M per sample, so even with only 10% recovery, I deemed I have enough reads to proceed with the analysis (my rarefraction graphs also seemed fine). Would it be okay to infer information from these data?
Thank you very much for your help!