dada2

dada2 copied to clipboard

Use of priors with ITS data

4

Dear all, we have an ITS dataset to analyse and there is a species of interest that we would like to be more sensitive in detecting. We can go into...

ramiroricardo

Creating Stacked Bar Chart using Dada2

4

Good day! Is there a way how can I create a stacked bar chart (i.e. 100% stacked bar chart) at the end of the pipeline? [barplot2 family.pdf](https://github.com/benjjneb/dada2/files/9288358/barplot2.family.pdf)

EJS01

Analyzing 2 batches of sequenced samples separately or together - using qiime dada2 denoise-ccs

4

Hi@benjjneb, I have 2 questions regarding the use of dada2 for PacBio ccs sequences. First, I have samples from the same tissue that have been sequenced using PacBio technology on...

emankhalaf

Issues with assignTaxonomy Function

4

Hi, I was wondering if anyone could help me figure out why the assignTaxonomy function isn’t running in my code. I know it can sometimes take a while to run,...

userJ123

Are there any tools that automatically detect where to truncate forward and reverse reads for 16S?

6

I'm trying to run DADA2 via QIIME2 and noticing that it's very hands-on and not completely automated. **Are there any reliable tools that can indicate where I should trim my...

jolespin

Mismatched forward and reverse sequence files...

16

Hello, I'm going through DADA2 on a publicly available dataset, and am running into this error. I have sorted both my filtered and unfiltered files and am still getting this...

chuynh96

Different sequence runs with different sequence lengths

8

Hello, I am relatively new to DNA sequencing analyses so I appreciate the detailed tutorials and feedback on previous issues. I have 16s rRNA data from 3 different sequence runs...

larajan67

Removing reads with zero length when cutting off the primer sequences using cutadapt in DADA2

2

Hi, I am running some scripts modified from DADA2 ITS tutorial(1.8). I used the following R scripts to remove the primers: cutadapt

Ecotone23

Assigning taxonomy and sequence table order

12

Hello, When testing taxonomy assignment I noticed that the output would change if the order of the sequences in the sequence table was different (this apparently was due to the...

max-mose-diversigen

Can DADA2 pipeline assign taxonomy for vertebrate DNA sequences?

2

Hi All, I am new to DADA2 pipeline and wondering if there is any database/package that can be used in DADA2 pipeline for assigning taxonomy for DNA sequences of vertebrates....

Ecotone23