Giovanni Bubici

13 Questions 80 Answers 0 Followers

Questions related from Giovanni Bubici

How can I get redundant FASTA reads from a file containing collapsed reads?

Input file (collapsed reads) is: >1-1TGCG>2-4ATAT>3-1TGGC>4-1TGAG>5-1TTCA I would like the output file as...

23 November 2016 6,034 7 View

How can incomplete factorial designs be statistically analyzed?

I would analyze such designs with one-way ANOVA, though I’m wondering whether factorial-ANOVA or nested-ANOVA can be used. The research question is the following: is the behavior of a parasitoid...

06 April 2016 1,170 10 View

How can I test statistically significant occurrence of Single Nucleotide Polymorphism (SNP) in case-control study of Next Generation Sequencing (NGS)?

A 'case' sample and a 'control' sample have been sequenced using Illumina platform. After bioinformatic processing, my database contains million of reads, each consisting of 3 nucleotide (codon)...

30 January 2015 9,543 20 View

What is the best statistical method to analyze data from multi-choice assays?

An insect individual is placed in a box that has 6 sectors, each holding a different food. The insect is placed in the center of the box, and it is free to go in any sector. After it enter into a...

16 April 2014 5,712 19 View

How can I perform a multivariate analysis of variance in a binomial distribution framework?

Commonly, I use the MANOVA statement in the GLM procedure of SAS (general linear models) to perform a multivariate analysis of variance on continuous dependent variables. Also, I use the statement...

15 April 2014 333 7 View

How can time proportion data be statistically analyzed?

For example, data consisting of a proportions with: - Numerator (time required to do something, in seconds) and Denominator (duration of experiment, in seconds) - Numerator (number of events) and...

11 December 2013 9,046 5 View

Can anyone provide some plant viral and fungal pathogen transformed with fluorescent proteins (GFP, YFP, RFP, BFP)?

I am interested in: CMV-GFP, CaMV-GFP, Verticillium dahliae-GFP and Pyrenochaeta lycopersici-GFP.

10 October 2013 177 0 View

Which freeware software can be used to view alignment/mapping files be in Windows operating system?

I usually perform mapping of reads to reference genes or genomes using bowtie, that yield an output SAM mapping file. I can import and view such SAM files into CLC Genomics Workbench, but I'm...

08 July 2013 9,274 4 View

Can a kind of lethal dose (e.g. LD50) be calculated for a continuous variable such as speed?

We know that LD50 is the dose of a chemical able to kill 50% population of an organism. I wonder if the same concept may be used for a growth speed. In particular, I would like to know if a LD50...

05 March 2013 4,009 12 View

Can standard deviation and standard error be calculated for a binary variable?

In a graph showing the progress over time of the probability to find a pathogen within plant tissues, I'm wondering if standard deviation or standard error bars can be added. The probability to...

08 February 2013 2,409 48 View

How can assumptions for ANOVA be tested for a factorial experiment?

I would like to test the normality of data and homogeneity of variances for a factorial experiment. For example, given three fixed crossed factors i.e. A, B, C, with 3 replicates (1,2,3). Should...

15 November 2012 9,127 7 View

Which is the most appropriate method to analyze counts?

I would like to analyze data where the dependent variable is a count and the independent variables are categorical. The count is the number of positive events out of the total. Which method when...

05 October 2012 10,002 90 View

What recent papers focus on the biocontrol of soil-borne plant pathogens with Streptomyces in the field?

I work on biocontrol of Verticillium dahliae and Pyrenochaeta lycopersici with Streptomyces. Although the huge literature on Streptomyces, I couldn't find sound results on field biocontrol, while...

07 July 2012 2,660 1 View