Comments (10)
That being said, a new method would let us re-use this elsewhere...
from q2-dada2.
If I am not wrong, the 100% clustering of ASV can also be performed using q2-vsearch plugin ? So maybe there is no need to add a specific condition in q2-dada2 script?
What do you think?
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I suspect the latter is what we're looking for, since it sounds like the forum user was interested in combining subsequences together. I'm a little curious as to what minOverlap
is for, since it seems like we're dealing with +- a few nucleotides, so having a subsequence of only 20ish sounds pretty bad (and will probably bin into the most abundant read no matter what).
from q2-dada2.
To "qiime" in, if this is something that is going to be integrated into the workflow commands, this may be best left until we migrate the plugin to the version 1.8 of the dada2 R package, as I am expecting to overhaul the q2-dada2 R scripts a bit at that time.
p.s. we are waiting on bioconda updates for that migration to happen: #85 (comment)
from q2-dada2.
I can take this one 👍
from q2-dada2.
How would we want to implement this? That doesn't appear to be a parameter, but a standalone function within the dada2
package.
collapseNoMismatch <- function(seqtab, minOverlap=20, orderBy="abundance", vec=TRUE, verbose=FALSE)
By expose is it adding a new method to q2-dada2
, or having this flag run it using strictly the default parameter values?
from q2-dada2.
that forum post seemed to suggest that this was a parameter, so that was my assumption when I opened this issue without further investigation.
I like the new method idea though.
from q2-dada2.
I'm not sure the best way to handle adding the function inline w/ denoise, as it'd require the flag to run it or not and also a flag for the overlap parameter - assuming all the other default values are fine to use. I'll start with just the function I suppose. Would joining them have to be a pipeline then? It could always be added inline to denoise as well and keep this as a separate function. ¯\_(ツ)_/¯
from q2-dada2.
I'm not sure the best way to handle adding the function inline w/ denoise, as it'd require the flag to run it or not and also a flag for the overlap parameter
I think this would be conditionally run in the R scripts, right (like the chimera checking section)?
from q2-dada2.
I'm a bit uncertain if our implementation of de-novo will cluster shorter sequences or not. Also, the IDs are something to consider, but I don't see why these couldn't be made to be very compatible.
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Related Issues (20)
- Add more DADA2 parameters to the wrapper HOT 3
- Allow denoise-single to process either reverse or forward reads HOT 3
- Add long-read support HOT 27
- Certain ID schemes can become mixed up with barcodes during sorting HOT 3
- I've gone through tutorials and forums and still don't understand how to select the truncLen and trim parameters in dada2 HOT 1
- denoise-paired: add % merged to stats output
- expose minOverlap parameter HOT 10
- denoise-paired: expose matchIDs parameter HOT 3
- Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) HOT 13
- Update denoise-paired document from minimum overlap 20 > 12nt
- Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin HOT 1
- dada2 justConcatenate HOT 6
- Update to latest DADA2 for R 4.0 support HOT 1
- dada2 drops samples without reads unfiltered reads from table but not denoising stats. HOT 1
- Restructuring dada2 R/python code
- error while using dada2 in qiime2 HOT 1
- ENH: include error model plots in denoise-* output HOT 3
- Importing DADA2 R rep. sequences into QIIME2 HOT 1
- Can not run qiime dada2 denoise-ccs without primers or adapters HOT 4
- Add warning when pooling method and chimera detection method are misaligned HOT 1
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