https://divingintogeneticsandgenomics.com/tags/coordinates/ Recent content in Coordinates on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 30 Apr 2015 14:57:00 -0700 https://divingintogeneticsandgenomics.com/archive/get-all-the-promoter-sequences-of-human-hg19-genome/ Thu, 30 Apr 2015 14:57:00 -0700 https://divingintogeneticsandgenomics.com/archive/get-all-the-promoter-sequences-of-human-hg19-genome/ One of my former friends (a biologist who does not know much about computer) wants me to help her to get all the promoter sequences from the human genome. It is a very simple task and I think all the biologists should know how to do it. There are many ways to do it, but I will show you how to do it using bioconductor. View this gist on GitHub https://divingintogeneticsandgenomics.com/archive/fetch-genomic-sequences-from-coordinates/ Tue, 24 Feb 2015 08:19:00 -0800 https://divingintogeneticsandgenomics.com/archive/fetch-genomic-sequences-from-coordinates/ One of the most common tasks in bioinformatics is to retrieve DNA sequences according to the given coordinates (in bed format or others). I had a post previously to describe this, and if you google around, you will find many other methods. I am going to compile all the methods that I found in this post. Please refer to the posts in biostar: https://www.biostars.org/p/19267/ https://www.biostars.org/p/3137/ https://www.biostars.org/p/56/ Method 1: Using DAS server https://divingintogeneticsandgenomics.com/archive/understanding-the-forward-strand-and-reverse-strand-and-the-coordinates-systems/ Thu, 07 Aug 2014 09:05:00 -0700 https://divingintogeneticsandgenomics.com/archive/understanding-the-forward-strand-and-reverse-strand-and-the-coordinates-systems/ we are on day 4 of the MSU NGS course. In the morning, instructor Istvan introduced Genomic Intervals. To understand the coordinates system, one needs to understand the strandness of DNA. sense strand is the coding strand anti-sense strand is the reverse-complementary strand of the coding strand see details below: https://www.biostars.org/p/3423/ https://www.biostars.org/p/3908/ again, everything is on biostar :) I drew a picture to better understand it remember: coordinates are reported 5'---> 3' forward strand