Quick Start Guide#

This page offers straightforward quick-start information on using LiftOn to map RefSeq v110 annotations on chr22:1-50755568 from GRCh38 version 40 patch 14 to T2T-CHM13 v2.0. If you haven't already, please follow the steps outlined on the variant page to install and load LiftOn.

Before you get started, make sure you have already cloned the LiftOn GitHub repository. We provide an example in test/lifton_chr22_example.sh.


Super-Quick Start (one-liner)#

LiftOn maps annotations from one assembly to another. To run LiftOn, all you need are three files:

  1. A target assembly (Genome \(T\), FASTA Format): chm13_chr22.fa

  2. A reference assembly (Genome \(R\), FASTA Format): GRCh38_chr22.fa

  3. A reference annotation (Annotation \(R_A\), GFF3 Format): GRCh38_chr22.gff3

Run the following commands:

$ cd test

$ lifton -g GRCh38_chr22.gff3 -o GRCh38_2_CHM13_lifton.gff3 -copies chm13_chr22.fa GRCh38_chr22.fa

After this step, you will obtain an annotation file GRCh38_2_CHM13_lifton.gff3 in GFF3 format, and a directory lifton_output/ that contains various outputs, including sequence identity scores, unmapped features, extra copies, intermediate files, and more. We provide further explanations of the output file hierarchy in the output files section.


Try LiftOn on Google Colab#

We created a reproducible and easy-to-run LiftOn example on Google Colab. It's a good starting point, so go ahead and check it out!

https://colab.research.google.com/assets/colab-badge.svg

Congratulations! You have successfully installed and run LiftOn. For more detailed analysis explaination and file format, please check:

See also