Identification of gene based on GWAS marker

More Widya Pintaka Bayu Putra's questions See All

Point cloud from google street view?

can we build point cloud from google street view? to step 3D models result

22 November 2023 5,763 0 View

The evolution of deep social mind in humans associated with use of tools in hunting and gathering ?

Are the cognitive aspects of early human society associated with its direct impact on logic and reasoning in tool making, hunting strategies, and social cooperation? While Chris Stringer's...

23 July 2023 7,594 0 View

What to do if my emission rate value is very low AERMOD can't plot it?

I have an emission rate data of PCDD/F, however it is very low (ex: 2,13E-10 g/s). If I put this value then AERMOD couldn't create a plot saying that the value is 0. What can I do?

18 July 2023 7,994 1 View

Why can mental disorders be influenced by genetic or hereditary factors? how did it happen?

what kind of factors that make it happen? how does it work?

10 June 2023 5,413 1 View

What is the relationship between tomoxifen treatment with chemotherapy in breast cancer?

I have a molecular biology assignment on breast cancer treatment, I hope you can help.

08 June 2023 7,302 5 View

Why do we only use the first control input and throw the rest on the MPC?

I am doing a Linear MPC and I still don't get why we need to throw the rest of the control inputs that we get from solving OCP inside the MPC. In my opinion, why don't we use the second and so...

09 April 2023 2,956 3 View

Why the quinone group was automatically converted to hydroquinone when I input the SMILE to ADMETLab2.0?

The SMILE of the compound is [COC1=C(C)C(=O)C2=C(C1=O)C1CN(Cc3ccsc3)C(C#N)C(C2)N1C], and it translated into correct quinone-containing compound in other web/program. But, when I input that SMILE...

20 March 2023 9,677 6 View

How to set up the format file for GAPIT software ?

Dear resrarchers who work in GWAS I have two PLINK file formats of map and pad. My question is, can both file formats use in GAPIT software? If not, how to change both file formats to suitable...

10 January 2023 2,776 2 View

Why docking results of two novel ligands can give same binding affinity but different protein-ligand interaction?

I carried out docking using AutoDock Vina for two new ligands at the active site of Bcl-2 protein. The two ligands only differ with one functional group (ligand A possesses OH, ligand B possesses...

03 April 2022 8,448 3 View

How to compute a Manhattan plot in Tassel ?

Dear researcher, I have 50 genome sequence of cattle but only 35 sequences that have a phenotypic data. Can I compute a Manhattan plot with an unbalance data like this with Tassel ? Thanks ...

14 November 2021 9,746 6 View

How to estimate sample size for GWAS of continuous and discrete traits? What are the pre-requisites?

Genome-wide association study (GWAS) Continuous traits: eg. Height Discrete traits: eg. Eye color

28 July 2024 286 0 View

What is the 'Effect' Column in GWAS Results?

Hello, I received some GWAS results. There is a column for SNP, position, REF/ALT allele, p value, SE, which is pretty straightforward. However, I am confused about the column titled 'Effect',...

03 May 2024 308 1 View

Could anyone share with me a protocol for a GWAS in plants, please. Thank you :)?

I am going to work with A. thaliana, but I am starting to get involved with the technique. Thank you!

13 April 2024 6,003 1 View

How to get the annotation file of the Immunochip array?

Dear community, I'm inputting data from an old GWAS study based on the Immunochip array, and I need the annotation file to conduct a few QC steps. I can't find it on the Illumina website; I...

06 April 2024 8,979 2 View

Is there any available software that can be used to run meta-QTL analysis?

I want to run a meta-analysis for linkage mapping and GWAS QTLs and I will require a software to be able to achieve this.

18 February 2024 264 3 View

How to find SNP point of a SilicoDArT marker in bread wheat genome?

Hi all, I have a set of SNP and SilicoDArT marker data. The SNP points of SNP markers were already provided by the GBS company (Such as G>T). However, the SNP change points (allele change, such...

31 January 2024 5,834 0 View

Who uses GWAS (genome-wide association) & candidate Gene ?

I want to know what is more recommended for Specific SNPs (single nucleotide polymorphism) Who has good experience, What is more recommended GWAS or candidate gene? for Specific SNPs in specific...

29 November 2023 5,337 1 View

Hello! I am working GWAS. I am facing a problem while performing the GLM model. Thus, may I have solution from the specialist?

myY

27 November 2023 952 0 View

Is the SNP significant for the phenotype or is it a false positive?

I performed an analysis for a specific gene/region of interest using GWAS summary statistics for a binary phenotype (+/- disease). Using the corrected p values in the summary statistics and...

05 November 2023 9,886 3 View

Suitable Models and methods for GWAS in plants?

Hello dear researchers, Which methods and models are suitable for GWAS in heterosis population in plants? Which methods and models could be used for GWAS in inbred population in plants? and also,...

25 October 2023 2,292 0 View

Ahmed Mousbah

Read the following article in BMC genomics

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6324-7

Good Luck

Widya Pintaka Bayu Putra

Thanks very much. I can do it now...

Pascal Rihet

You could use the VEP tool (ensembl web site) to get the position within (or outside) the genes, and the GTEX portal to check whether the SNP is an eQTL and to identify its potential target genes.

Thanks very much