Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011

(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

I’m working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I’ve sequenced the region in a small sample, I’m picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab will need flanking sequence.

This is easy to get for SNPs in dbSNP, but what about novel SNPs? Specifically, given a list of genomic positions where

To leave a comment for the author, please follow the link and comment on their blog: Getting Genetics Done. offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Tags: , ,

Comments are closed.


Mango solutions

plotly webpage

dominolab webpage

Zero Inflated Models and Generalized Linear Mixed Models with R

Quantide: statistical consulting and training




CRC R books series

Six Sigma Online Training

Contact us if you wish to help support R-bloggers, and place your banner here.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)