Manuel Ochoa

6 Questions 2 Answers 0 Followers

Questions related from Manuel Ochoa

Does keeping primer sequences affect downstream analysis of 16s sequences?

Hi all! I have some 16S sequences amplified with the universal primers 341F: CCTACGGGNGGCWGCAG & 805R: GACTACHVGGGTATCTAATCC. I have checked the sequences and primers are present in all...

23 January 2023 5,348 3 View

Primer removal during 16s sequencing?

Hi all! I have paired end reads of the V3-V4 region of the 16s. PCR amplification and sequencing was performed at macrogen facilities, in Korea. Sequencing was performe with Illumina MiSeq. I...

12 January 2023 3,701 1 View

Experiences with MP BIO DNA kit contamination?

Hi, there Does anyone has experience with (MPBIO) FastDNA spin Kit for soil DNA extraction intrinsic contamination? Salter et al. 2014 test it, and it had several intrinsic microbial...

21 November 2022 7,167 0 View

Troubles with qiime2 biom export file?

Hi, all! I have generated a biom file in qiime 2, which I am trying to export to R, with the phyloseq package, yet without success. What I have tried is: biom = system.file("extdata",...

15 September 2022 5,412 0 View

Is it appropiate to use a neighbor joining tree to calculate unifrac distances?

Hi all, I have 16s sequences from the V3-V4 region. I was wondering if it is correct to use a neighbor joining tree to calculate unifrac distances, instead of a maximum likelihood tree. Any help...

15 September 2022 5,292 1 View

Does qiime2 is restricted to analysis of short 16s?

Hi all, I was wondering if qiime2 is able to perform analysis with long 16s fragments, like those retrieved when you use universal bacterial primers 27F &1492 R, which generates a ~ 1500 pb...

11 April 2022 1,442 1 View