Valentina Vanghi

7 Questions 10 Answers 0 Followers

Questions related from Valentina Vanghi

Metagenomics: How to deal with replicate samples?

Hi, I have biological replicates: they come from the same raw sample (tube of sediment) but from different DNA extraction & sequencing experiments. These are metagenomes and I used whole...

30 June 2022 5,661 1 View

How can I figure out if the primers have been trimmed or not?

Hi, I sent some samples to a company to do whole genome sequencing (Illumina). Here below is an example of one of the fastq files I got from them. They told me that adaptors and barcodes have...

24 February 2022 5,092 3 View

(Kraken2 custom db) How to deal with the unmapped.txt file?

Hi, Has someone experience in building a custom db using Kraken2? I have downloaded the fasta files for some taxa and build the new db but it produced an unmapped.txt file with a long list of...

14 December 2021 4,097 6 View

Should a perform an assembly before alignment (with metagenome)?

Hi, with metagenome samples, with reads usually spanning from 3k to 5k after whole genome sequencing (Oxford nanopore), should I also perform the assembly step (flye) before the alignement (Kaiju...

02 December 2021 4,878 6 View

PCoA (not PCA) or NMDS?

Hi, I need to perform some comparative analyses with metagenomics data (abundances). I would like to know whether, in term of final result, using PCoA or NMDS really makes a big difference, and...

28 May 2021 3,646 3 View

How much DNA do you usually get from soil/sediment?

Hi, I would like to know how much DNA you generally get from soil and/or sediment. I did some extractions but I am not sure if what I have got can be considered a good amount or not. I use kits...

21 January 2021 636 2 View

How to increase the final DNA yield using the Qiagen PowerSoil DNA extraction kit?

Hi, I am having troubles trying to extract DNA using the Qiagen PowerSoil kit from cave sediment (mud/clay). I always get very low yield:

04 January 2021 5,209 1 View