Deblur joined end sequence

New to Qiime2, have a quick question about Deblur, the documentation emphasize deblur only take forward reads, not including reverse reads at all.
Will it treat JoinedSequencesWithQuality same as PairedEndSequencesWithQuality that only forward read are processed? or JoinedSequencesWithQuality is processed as SequencesWithQuality, the reverse read is processed as well?

Hi @zwei,
JoinedSequencesWithQuality reads will be treated like SequencesWithQuality. Joined reads have already been joined into single reads so from a human perspective we can consider these to be single-end reads (that’s what they’d look like if we export the artifact). From a machine perspective we apply the semantic type to ensure that these data are only used in an appropriate manner, so for example we cannot input JoinedSequencesWithQuality to dada2, which requires unadulterated single/paired-end reads.

You can read more about joining reads (and then denoising with deblur) here.

I hope that helps!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.