Dada2 minimum overlap

Ideas and Suggestions
,
1

Hi!
I was wondering, is there any way to set minimum overlap for merging the reads in q2-DADA2 for paired reads? Like minOverlap in R. Just to be able to compare the outputs with default 12 bases and custom parameter.

2

No there is currently no way to adjust this with q2-dada2, but it would be an easy fix. I have raised an issue to address this. Contributions are welcome and encouraged! :wink:

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3

Thx, I will try to do it as well :eyes:

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4

Hi!
I tried to modify this file /home/My_PC_Name/anaconda3/envs/qiime2-2019.4/bin/run_dada_paired.R and changed this part:

### PROCESS ALL SAMPLES ###
# Loop over rest in streaming fashion with learned error rates
denoisedF <- rep(0, length(filtsF))
mergers <- vector("list", length(filtsF))
cat("3) Denoise remaining samples ")
for(j in seq(length(filtsF))) {
  drpF <- derepFastq(filtsF[[j]])
  ddF <- dada(drpF, err=errF, multithread=multithread, verbose=FALSE)
  drpR <- derepFastq(filtsR[[j]])
  ddR <- dada(drpR, err=errR, multithread=multithread, verbose=FALSE)
  mergers[[j]] <- mergePairs(ddF, drpF, ddR, drpR, minOverlap=4)
  denoisedF[[j]] <- getN(ddF)
  cat(".")
}

by adding “mergers[[j]] <- mergePairs(ddF, drpF, ddR, drpR, minOverlap=4)”

Do I really changed parameters to run it with minOverlap 4 by this way?
In the output with the same data and the same other parameters I received more than 100 additional readpairs and about from 1 to 50 or more in most of the samples. And now I am wondering if it is because of the changes I did or it can happens by some other random factors?..
Thank you in advance.
PS wanted to add something like option
--p-minOverlap
to the command line options but it’s over my head to figure out everything I need to change (I am a beginner in python and coding and bioinformatics)

5

That looks correct to me. If you did not receive an error that is probably a good sign...

No worries — we will add this feature in a future release of QIIME 2. Thanks for the suggestion!

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