I would like to know if the sequencing data generated by Hiseq (2 X 250) and Miseq(2 X300) be treated as one dataset for the same study? If some samples from the study were sequenced using Miseq (2 X300) and now the other samples in the same study will have to be sequenced by Hiseq (2 X250), Is it ok to treat them uniformly. In such a case, what is the best possible way to obtain uniformity with QIIME2 analysis?
Sure, as long as the 2X250 reads contain enough overlap to join successfully.
Demultiplex and denoise each run separately, then merge your sequences and feature tables after denoising.
There is some concern, I suppose, that differences in read length/chemistry could subtly bias the results. Just be aware of that as a potential covariate if comparing sample groups that are exclusive to each sequencing run.
Sorry for the late reply.
Thank you. I will keep this in mind while analyzing my data.
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