Hi,

You can also use the biomartR package, it should not be so long. First, you should search for all genes at a certain distance from SNP positions, then you choose the one with the smallest distance.

Sometimes, I use the bedtools as well, it will be much quicker.

Best

Hi,

You first need to download text file of chicken genome assembly (I think from biomart). Then by writing a simple script in R you can do everything you need.

I remember that I wrote such script when working with cattle and sheep genome assembly to extract genes that located in vicinity of significant SNPs in my selection signature analysis. If your problem still remains, let me know to check if I have those scripts.

Hi,

As my friend Mr. Ghoreishifar and also Dr. Duy said, you can use R biomaRt package for this. You also can use the plink "--gene-report" command.

However, Here is a chunk of R code that helps you to find adjacent genes for your SNPs.

### Preparing Gallus Gallus Genes

library(biomaRt)

Gallus_Dataset = useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "ggallus_gene_ensembl",host = "www.ensembl.org")

genes = getBM(attributes = c("chromosome_name","external_gene_name", "ensembl_gene_id", "start_position", "end_position") ,mart = Gallus_Dataset)

genes$chromosome_name

Dear Anna Wolc, Dear Do Ngoc duy ,

Dear Mehdi Esmaeili-Fard , Dear Mohammad Ghoreishifar

Thanks a lot for your helpful answers.

Best Wishes

Pablo Fonseca has developed a great package for the SNP/QTL annotation in livestock species. You might have a look at it as well.

https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html

Dear Do Ngoc duy ,

This is exactly what I'm eager for.

But unfortunately, I could not apply the chicken database for it. The existence tutorial uses Bovine data.

I think the package work for other livestock species as well

First extract region related to you SNP list. Untill 500 region in each time is possible in biomart. With any need to write any script.

Then biomart could explor this genes for you. Then you could do gene network analysis, also.