Eman Khalaf

Failure when installing metacoder in RStudio in both windows and Ubuntu 20.04

2

Hi, I got this error when installing metacoder in windows: devtools::install_github("grunwaldlab/metacoder") WARNING: Rtools is required to build R packages, but is not currently installed. Please download and install Rtools 4.0...

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...

Zero read.out - 16S PacBio reads

2

Hi @benjjneb I have a new batch of sequenced samples that have been 16S sequenced using PacBio technology. I have two significant issues when processing the reads using DADA2 pipeline...

Duplication of Species column when using addSpecies function

19

Hi @benjjneb To assign the taxonomy of v4 sequences, I use 2 consecutive steps according to dada2 tutorials: `taxa

Error filterAndTrim applied on MiSeq reads

10

@benjjneb Hi, I used to manipulate MiSeq reads on Qiime2 where I can use DADA2 plugins along with other q2-plugins easily. I need to export the sequence data as fasta...

Error when running assignTaxonomy on PacBio 16S reads

15

Hi, I have 16S sequences generated from PacBio technology. When I ran: tax

Error when using Krona to generate hierarchical representation of Tax4Fun output??

10

Hello everyone, I would like to use krona to display Tax4Fun output: 0.008833584 Metabolism carbohydrate metabolism Glycolysis / Gluconeogenesis 0.006236372 Metabolism carbohydrate metabolism Citrate cycle (TCA cycle) 0.008593556 Metabolism carbohydrate...

DADA2 denoise of PacBio sequences produced Warning: NAs produced by integer overflow

7

Hi @benjjneb I am processing over 1000 16S PacBio SMRT sequenced samples using DADA2 workflow in R, and I got this warning message from dada step using pool="pseudo" : "Warning:...

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...

Phyloseq-Deseq2 (Error in dimnames(x)

7

Hi everyone, I wonder if any of you could help me to solve this problem. I have different sets of plant tissues with different treatments and I need to calculate...