How can I calculate Minimum variant allele frequency threshold?

15 September 2015 1 8K Report

varsacn have specified spme default values.i am trying to understand if we can use those default values for RNA data or need to calculate it separately

Bahman Fazeli-Nasab

you have to use botestain et al., 1980 formula

More Sameer Chaudhary's questions See All

What should a Mechanical Engineering PhD scholar focus on during their PhD to enhance their chances of securing a postdoctoral position?

29 July 2024 7,714 4 View

What is the maximum value of Divesity Gian in MIMO? For two antenna system its 10dB. As no. of antennna increse diversity gain increase or decrease?

Somewhere on the internet, it's reported the maximum diversity gain limit theoretically can be achieved is 10dB. Some papers said it increases with more antennae and some said it will decrease.

09 June 2024 5,121 2 View

To create a study area map for your research sites, which software is the easy and best choice for use in a scientific publication?

Any easy and best GIS software options?

15 May 2024 507 9 View

I need a topic or tittle which is depend on the any broking comapnay?

Currently I am working in the internship program at Arihant capital which is based on the trading and brokering the stock market. my college have made me resarch on the my internship organization...

12 May 2024 770 4 View

How does climate change intersect with illegal wildlife trade, and what are the implications of this relationship?

Looking for a research topic that involves the implications of climate change and illegal wildlife trade.

30 April 2024 3,252 1 View

Could someone explain me how to design an ITC experiment to get a result as quickly as possible?

Hi there, My area of research is an aqueous Zinc ion battery and my goal is to find the binding affinity and thermodynamic properties of Zn-ions binding with polyacrylic acid (PAA) by ITC...

30 April 2024 4,171 0 View

Could somebody tell me how can I prepare a polymer solution in terms of monomer concentration?

My objective is to find the binding affinity of divalent metal ions with polyacrylic acid (PAA) by Isothermal Titration Calorimetry. In this experiment, I need to prepare 2mM of PAA. The 2mM...

24 April 2024 9,090 2 View

Is the demand of oligonucleotides growing?

What is the approximate yearly consumption of oligonucleotides, including primers, probes, siRNAs, and custom DNA/RNA sequences, across all research institutions and biotech industries within...

22 March 2024 5,874 0 View

How can position 77 be associated with multiple types of genes, namely F, M, NP, and P? #Query about Genomic Position 77 and Gene Annotations?

During my analysis, I observed that genomic position 77 is annotated with gene symbols F, M, NP, and P across various transcripts. Please find the example below. I used the gff3 file from NCBI...

17 March 2024 1,643 1 View

Has anyone recently submitted at Nature Biomedical Engineering Journal?

I would like to have your experience, reviews and suggestions regarding the same.

12 March 2024 9,100 0 View

How do you assign allele numbers and sequence type after amplifying housekeeping genes by PCR for MLST?

How to assign allele numbers and sequence type after amplifying housekeeping genes by PCR for genotyping of S. pneumoniae strains by MLST using bioedit ?

19 July 2024 5,239 2 View

Genotype and allele distribution statistics ?

Hello, how can I do the statistics associated with genotypes and alleles as in the table? thank you very much for your attention.

17 July 2024 7,606 2 View

Chi-square test for allele distribution?

Hello, when calculating the p value for the alleles in the table, how do we place the values in the chi-square test in the four-eyed table? Thank you very much for your attention.

17 July 2024 998 2 View

Why band for normal allele appears in a sample that is confirmed homozygous mutant?

I use confirmed homozygous mutant and homozygous normal samples for tetraARMS PCR optimization. everytime I run amplified products on gel I observe three bands instead of two bands. DNA samples...

27 June 2024 8,403 3 View

Uncallable SNP showed significant to MTA, what to do?

I am getting a significant marker trait association for traits. But understanding the allelic association is difficult; NN is the missing allele. Can anyone help me?

13 May 2024 8,860 2 View

How to convert SSR allele scoring (bp) to rqtl/Joinmap format for linkage & parentage analysis (A, H, B, etc) ?

Hello, I am planning to conduct linkage and parentage analysis using microsatellite markers (SSR). The scoring process has been completed with output in allele size (bp) format. The analysis is...

12 May 2024 5,329 0 View

Is there any published article about the effects of using a minor allele frequency filter on the quantity of missing data per individual?

I performed two RAD-seq assemblies using ipyrad. I filtered the outputted .vcf file of each of the two assemblies using vcftools to limit the maximum quantity of missing data per locus to 60%. To...

12 March 2024 2,136 0 View

What are the best HW p-value & MAF cutoffs based on my study ?

Hello, Based on my research question, I would like not to exclude variations that are out of Hardy-Weinberg equilibrium, and I also want to have rare variants in my study ( i mean the MAF...

07 March 2024 5,788 0 View

Does same gene dose mean same amount of expression?

My question is on the way of expression of allele specific copy number variation, e.g. individual 1 has a CNV as 3, 3, on each allele, with 6 copies; and individual 2 has 1, 5, on either allele,...

28 February 2024 1,598 1 View

Sample size calculation for validating a new test against gold-standard?

Dear Friends! The gold-standard for identifying an allele for human leukocyte antigen is SBT or sequence-based typing. If I devise a new PCR test or LAMP test, how many known positive and negative...

16 February 2024 7,953 1 View