What is LiftOver? |3 Methods to Convert Genome Coordinates Efficiently
▸ Welcome to my comprehensive guide on LiftOver and genome coordinate conversion methods! In this video, we'll explore the concept of LiftOver, a powerful tool for converting genome coordinates between different assemblies. In this video I explain what is #LiftOver, when to use and when NOT to use and demonstrate three efficient methods for converting genome coordinates using LiftOver and similar tools.
Method 1: UCSC Genome Browser
Method 2: Command Line Tools (CrossMap)
Method 3: R/Bioconductor Packages
By the end of this video, you'll have a solid understanding of how to use LiftOver to seamlessly convert genome coordinates and enhance your bioinformatics workflows. Don't forget to like, share, and subscribe for more insightful tutorials! I look forward to your comments under the comments section!
▸ R script - rtracklayer
https://github.com/kpatel427/YouTubeT...
▸ What is the difference between hg19 and hg38?
• What is hg19/hg38? - All you need to ...
▸ Using Conda and virtual environments
• Demystifying Conda (Anaconda, Minicon...
▸ SNP conversion FAQ by UCSC liftOver
https://genome.ucsc.edu/FAQ/FAQreleas...
▸ CrossMap vignette
https://crossmap.readthedocs.io/en/la...
▸ 0 based and 1 based coordinate system
https://www.biostars.org/p/84686/
Chapters:
0:00 Intro
0:37 What is LiftOver?
2:11 Using UCSC LiftOver: When to use and When NOT to use?
4:23 Sources available to convert genomic coordinates across assemblies
6:37 Method 1: Using LiftOver on UCSC genome browser
9:33 Method 2: Using CrossMap
13:08 Method 3: Using R package: rtracklayer
Show your support and encouragement by buying me a coffee:
https://www.buymeacoffee.com/bioinfor...
To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
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