dada2

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Added parallelization in filterAndTrim for Window OS via PSOCK sockets.

cylyau

Aborted R session with DADA2 run for a large number of PacBio-sequenced samples

11

Hi, I have ~650 16S PacBio sequenced samples and am following the DADA2 tutorial for PacBio reads. I successfully used this tutorial with different projects, but given the large number...

emankhalaf

The lengths are different between dereps an dadas

10

I would like to do the data preprocessing: from fastq to ASV and I faced problem when I conducted merging paired reads. ```{r quality_filtering} # Load raw fastq files fastq_files

suzywang116

Question about reverse complement in assignTaxonomy

2

Hello! I have a question about the tryRC argument of the assignTaxonomy function. For those representative sequences that their RC gave a better match, shouldn't then be replaced by the...

mtsiknia

denoise-ccs for ITS

1

Excuse me, We are using denoise -ccs to denoise a set of ITS full-length PacBio CCS sequences, do you have the suggested p-min-len and p-max-len values ? Thank you.

Hobgoblin8

quality filter: imbalance forward vs reverse reads - dada2-

1

Hello! I'm performing quality filtering on my sequences due to low quality in the reverse reads. However, I've encountered an imbalance where I have fewer reverse reads compared to forward...

valengirardi

Solving the "Error: BiocParallel errors" (in almost every sample)

3

Hi, I am an undergraduate studying bioinformatics in the microbiome analysis field, and I am having a BiocParallel Error every time I run my code for the ENA database datasets....

Yoonseopark02

Increasing number of nonchimeric reads compared to the number of input reads

8

Hi everyone I was using dada2 in R on my arbuscular mycorrhizal fungi reads and I noticed that after truncating them, I got an increased number of nonchimeric reads compared...

Abdelrahim-maker

Clustering dada2-obtained ASVs into OTUs with DECIPHER

4

Hello, I have a phyloseq object that I obtained with the dada2 pipeline. I would like to cluster those ASVs into OTUs. For that, I have the following code (just...

ConstanceBtd

dada2 reference database for eukaryotes

1

Hi, may I know what dada2 formatted reference database you would advise to use for COI for arthropods? Thank you!

eunicetan