LOW percentage of input merged

Hi everyone, I would like to ask why the splicing rate between the left and right ends of my data is only 1%, and what are the possible reasons for this result? (Experimental and raw letter analysis) And how can we improve it?

sequencing region: 16S rRNA gene V4 (515F ,806R)
illumina PE150

Looks like you are loosing most of the reads at merging step. That's means that youre reads do not overlap. Solution will be:

  1. Reconsider truncation parameters (set it to higher values)
  2. Decrease minoverlap in Dada2 parameters
  3. If nothing works use only forard or reverse reads for the analysis.


Thank you for your prompt reply, I'll go back and try!

For solution No.3, Which one should I use for subsequent analysis, and will there be a big difference between the forward and reverse reads?

It depends on the quality plots and region targeted. Usually I just go for forward reads. Note that using only one read (F or R) may lead to poorer taxonomy annotations, so I use it only when there is no other way to improve merging stats.


1 Like

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