Giulia Trauzzi

12 Questions 12 Answers 0 Followers

Questions related from Giulia Trauzzi

Adjustment for multiple testing on confidence intervals?

Hello everyone, I calculated some pairwise FST estimates with hierfstat (pairwise.fstWC function) in R on my SNP dataset and then calculated confidence intervals (not p-values) on those...

28 May 2023 5,648 4 View

Why does the RDA (vegan) fail to calculated GIF for all variables?

Hello, I am trying to run an RDA using my 11 environmental variables and genomic data set. I have noticed that the genomic inflation factors are not calculated for all variables (the last three...

28 February 2022 977 0 View

Pophelper for STRUCTURE RUNS results?

Hello, I am using Pophelper in R to run the algorithm implemented in CLUMPP for label switching and to create the barplots for the different K (instead of DISTRUCT). I am getting a warning...

24 November 2021 8,492 1 View

Are 100 bootstraps enough when calculating FST, FIS and corresponding CI for a SNP data set ?

I am calculating the FST (overall and pairwise) and FIS (overall and per site) estimates and corresponding confidence intervals (CI). The functions I am using in R (from hierfstat) allow me to...

21 October 2021 1,422 1 View

How do I set the number of replicates per K run in STRUCTURE from command line?

Hello, I have been running STRUCTURE from the command line on my SNP data set. I cannot find a way to set the number of replicates per K run. Should I just run the same script multiple times?...

11 October 2021 2,649 0 View

Bayescan does not detect any outliers?

Hello, I am working on a SNP data set (generated via STACKS de novo) and, after testing for linkage disequilibrium using the R package genetics, I have tried 2 different methods for outliers...

18 June 2021 770 3 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...

23 February 2021 10,152 3 View

How can I calculate pairwise Fst values using mtDNA sequences?

I would need to obtain a matrix showing the pairwise Fst values for a bunch of populations using mtDNA sequences (from NCBI). I have never done this before so I am not sure whether there is a...

11 January 2021 2,211 1 View

Anyone having problems with low DNA concentrations after RNase A treatment (during DNA extraction)?

I am currently testing the GeneAid DNA extraction kit on abalone (Haliotis iris) attachment muscle tissue samples and it was working pretty fine, until I added the RNase A treatment (as stated in...

27 January 2020 3,171 1 View

Has anyone used a 10 mg/ml RNase A for RNA removal during Qiagen Blood&Tissue DNA extraction kit?

The protocol states that the concentration of RNase A required should be 100 mg/ml, but 10 mg/ml is the only one I have at the moment. So I was wondering whether any of you had tried the same kit...

18 November 2019 1,031 2 View

Do earthquakes lead to a shift to homogeneous habitat in the marine environment?

Hi, I was going through some papers, and I was wondering whether I could say that events like earthquakes might lead to a more homogeneous underwater habitat than before the earthquake itself. For...

01 January 1970 8,244 3 View

Is it possible to detect cross-contamination of samples (Illumina sequencing) only when analysing the outlier SNPs after SNP calling and filtering?

Analysing neutral SNPs = everything makes sense from a population genetic structure point of view. When analysing the outlier SNPs (that come from the same pool of SNPs called using STACKS) sites...

01 January 1970 4,414 2 View