Converting coordinates using LiftOver from GRCh37 to GRCh38

Question

[Nabila]

I have circular RNA coordinates from GRCh37 and i want to convert it to GRCh38 using LiftOver. I am not yet comfortable with doing it by R or Terminal. After doing it simply in my local computer, my coordinates are not the same as my supervisor's one. What might be the reason? Do I need to download fasta or gtf file or anything else?

I am simply using this link below and putting in my coordinates: https://genome.ucsc.edu/cgi-bin/hgLiftOver

[Pierre Lindenbaum]

my coordinates are not the same as my supervisor's one. What might be the reason?

wrong coordinates (0-based vs 1-based intervals Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems ), wrong chain file, not the same treshold, not the right file.

Answer 1

[Thind amarinder]

Take a look at this post Liftover vs Ensembl Crossmap. hg19 regions to hg38 using UCSC LiftOver and CrossMap ( on Ensembl).