Using the UCSC Liftover Webtool to Perform Liftover Analysis (Ex.: Rat rn5 to Human hg38 Genome)

Описание: Please note that in this video, Saniya shows ye how ye can use the free UCSC webtool (https://genome.ucsc.edu/cgi-bin/hgLif...) to perform liftover analysis to transform DNA genomic coordinates from a species and/or assembly to another species and/or assembly. That is, Saniya works on a toy example of 28 DNA regions (Chromosome #: start - end) in a rat dataset. We know the data is from the rn5 dataset where rn refers to rat and 5 is the version #. Since we are interested in mapping those regions back to a human genome (to analyze in humans), we need to do liftover analysis. Now, there are many different human genome versions available (e.g. hg18, hg19, hg38, etc.) and Saniya wants us to map to hg38.

Sometimes, the UCSC tool may not be able to do the conversion right away from rn5 coordinates to hg38 and thus sequential steps may be needed. Saniya explains how to do the conversion in 2 steps: 1. rn5 to hg19 and then 2. hg19 to hg38.

Thus, we leapfrog from rn5 to hg19 to hg38. How do we interpret the results from UCSC webtool? Saniya explains it all :)

Please note that Saniya uses 0.1 default for Minimum ratio of bases that must remap. As this value increases (near 1), then the rows that are mapped from the original file to the new file (after liftover) may decrease as the criteria for mapping becomes stricter. That is, if we set this value to 0.6 for example then we may get even fewer than 12 rows that map from rn5 to hg19 in the first step, and even fewer rows if we had a value of 0.8, etc.

In case the hg19 and hg38 concepts for the human genome (different assemblies) is confusing, please do check out my video on determining reference builds and why they matter (especially relating to hg19 and hg38):    • Liftover to Map Genomic Coordinates Betwee...  

In this way, we can map from rn5 to hg38. In the process, some regions may not be mapped and that is alright as rats and humans do have a lot of differences (sadly in Stuart Little's case, he was a brother though a mouse).

Given that this is a nice and neat webtool, no programming is needed! However, there are some downsides (like sequential approaches needed for some conversions).

Saniya does have another video related to performing liftover analysis in R using the Rtracklayer package here:    • Liftover to Map Genomic Coordinates Betwee...  

Please do subscribe to Saniya's YouTube channel and please do reach out with any and all questions, comments, suggestions, and beyond! :)

Also, if you would like to "buy me a cup of coffee" as a thanks, I would really appreciate it (even more so especially as I am still a student living on a stipend): https://www.buymeacoffee.com/saniyakh...