dada2

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Hi, I'm using ITS dada2 pipeline on two of my runs. In primerHits step, I got wired results for both runs: Run1: Forward Complement Reverse RevComp M768.FWD.ForwardReads 0 0 0...

Leran10

After Clustering ASVs of DADA2, what exactly to deal with the New OTU table?

3

Hi, I am new about metadata, I am trying to follow the pipe ITS of Dada2, and I got the ASVs table, but I want to cluster the ASVs to...

fenglong616

mergeSequenceTables()

6

Hi Ben, I have to analyze >20 runs and for each run I used (separately) dada2. I would like to combine them using mergeSequenceTables(). Many times, the different persons that...

ntromas

filterAndTrim object retains all sample names

1

Dear Dr. Callahan, I am processing Miseq v3 600 PE data for the 16S V3-V4 region (319F, 806R). I used cutadapt to remove heterogeneity spacer/primer at the 5'-end. What remains...

vanormbr

High loss of CCS reads in filtering step

4

Hello! In my current project, we used DADA2 on a set of 16S Full-length PacBio CCS reads including the Zymo Mock sample. Read tracking showed that I lost ~50% of...

effelsbn

Problem with taxonomic assignment?

2

Dear @benjjneb, I ran DADA2 on my microbiome data and got an issue with taxonomic assignment. I am working with synthetic microbial community so used customized database (full length 16S...

rahulnccs

INCREASE in reads following merging

1

Hello, I've been successfully using a version of the dada2 pipeline customised to our samples, but in my latest run it looks like the number of reads INCREASES following merging...

rosieeccy

Consequences of using dada2 on NovaSeq data

48

Hello, We have an amplicon dataset from a NovaSeq run and are exploring how we might alter settings in the dada2 pipeline to effectively identify errors in our data. In...

hhollandmoritz

filter low quality reads out of dada object

1

Hello, I noticed that after the denoising step, some reads in the dada object have low quality, and I would like to filter them out in a paired manner, so...

marie-vallier-valbiotis

Matching between Silva original sequences (138.1 release) and formatted files on zenodo.org

6

Hi! there is official taxonomy on Silva database https://www.arb-silva.de/no_cache/download/archive/release_138_1/Exports/ and there is your reformatted sequences https://zenodo.org/record/4587955#.YfPkvuormUn if I will take this file from Silva --- "SILVA_138.1_SSURef_tax_silva.fasta.gz" it will contain 10...

cppjocker