How To Convert Snp haplotype Data Into 0,1 Matrix? Which software or package is better?

More Farhad Alizadeh's questions See All

Does the genetic difference between populations increase with increasing geographic distance?

Hi everybody What is the relationship between the population's genetic and geographic distance? I appreciate your help. Best regards

01 February 2020 4,943 9 View

Why is it important to consider the background linkage disequilibriu (LD) between markers in inferences admixed population into different ancestries?

Hi everybody I want to study the inference of the admixed population into different ancestries but I can't understand why it's important to consider the background linkage disequilibrium (LD)...

10 November 2019 1,221 4 View

Is classification the genomes of an admixed population into different ancestries a good topic for my thesis?

Hi everybody I am a Ph.D biomedical engineering student. My project is about genetic ancestry. I want to work on classification the genomes of an admixed population into different ancestries. Can...

05 June 2019 9,617 7 View

How to run shapeit software?

Hi everybody I downloaded the shapeit software from the University of Oxford website. Now I want to install the software. I placed it in the Downloads folder. Here is my command. tar -zxvf...

05 June 2019 8,753 5 View

How can I access SHAPEIT2?

hi everybody, I want to use SHAPEIT2 in the my thesis for phasing. I have only a little information about bioinformatics and SHAPEIT2. I want to use freely SHAPEIT2. Best regards

03 April 2019 6,078 3 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View

If we are using snowball sampling technique, how do we justify the true representativeness of the sample statistically? is there any statistical test?

Are there any statistical methods to justify your sampling technique using SPSS or AMOS?

05 August 2024 9,153 4 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

How to report results of Generalised Linear Mixed Models in a journal article?

Hi everyone, If you have written or come across any papers where Generalised Linear Mixed Models are used to examine intervention (e.g., in mental health) efficacy, could you please share the...

04 August 2024 4,130 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Why 3 replicates for most biological assays? Is it enough to examine the data fits normal distribution?

Just bounced on me. Before statistically analysing significant difference, shouldn't we see if data fits normal distribution first? Is 3 replicates enough to testify the hypothesis of normal...

31 July 2024 8,141 13 View

Posthoc test lettering in JAMOVI?

Does anyone know of a module for the JAMOVI software that is capable of generating mean separations using the classic letters based on post hoc results (e.g., Tukey test)? If, as I believe, such...

31 July 2024 3,333 4 View

Which statistical test should we use?

N=6 Comparing pre and post test likert scale responses. Participants are mix of practicing & preservice teachers.

30 July 2024 7,233 4 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

Kai Wang

Maybe, you can convert genotype to 0 when it same as reference, if not convert to 1.

Chainarong Amornbunchornvej

Have you ever tried TASSEL [1]? You can use the "data-> numerical genotype" function to convert your SNPs data into a probability that an allele selected at random at a site is the major allele. So, it will give you 0,0.5,1 values for each site. I hope this helps.

[1] https://www.maizegenetics.net/tassel

Farhad Alizadeh

thanks for your help, Kai Wang and Chainarong Amornbunchornvej .

I haven't tried TASSEL yet but I'll try it soon.