-
If a representative sequence is present in a mock community (and hence the expected taxonomy file) but is not classified by some taxonomy classifiers (ahem... current sklearn naive-bayes), the eval th…
-
I am analyzing ITS1 amplicon data using DADA2 and the UNITE reference database. Last week I had an issue where the assignTaxonomy function was labeling ASVs as outlandish taxa (telling me I had marine…
-
Hi,
I am running Figaro via docker. The runs start ok but keep finishing with an error message:
Traceback (most recent call last):
File "/opt/figaro/figaro/figaro.py", line 218, in
mai…
-
# Issue Report
## Please describe the issue:
Dorado basecall identified the barcode without trimming, but subsequent demux also did not trimm reads. Is this the expected behaviour? Is it possible …
-
Hi,
Thank you for your continued development of Cutadapt -- often my go-to tool for processing different types of sequence datasets.
Now, I am trying to utilize multiple adapter trimming capabil…
-
Hi,
Will the current version of dorado take barcodes into account when identifying duplex pairs, or does this need to be done separately and provided with the `--pairs` option to `dorado duplex`?
…
-
Is there a limit to how many reads that can be processed in ClusterAmplicons.py? Without much testing, it appears that if I exceed 50K reads (or so; no finer resolution tested) the following invocatio…
-
Hi @benjjneb and community,
I'm running through the [standard DADA2 pipeline](https://benjjneb.github.io/dada2/tutorial.html) but lose >50% of my reads at the merging step. The sequencing setup was…
-
Hi, I'm a big fan of this software but was wondering if it might make sense to provide the option to threshold based on a false positive rate instead of error rate (similar to what SeqPurge does using…
-
I keep seeing the presence of an unknown taxa with the name "V1" anytime I construct my taxa bar plots. However there is nothing in my taxanomy.tsv file that traces back to this "V1" taxa and it seems…