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What is UCSC LiftOver?

What is UCSC LiftOver?

UCSC liftOver: This tool is available through a simple web interface or it can be downloaded as a standalone executable. To use the executable you will also need to download the appropriate chain file. Each chain file describes conversions between a pair of genome assemblies.

How do I download HG19 reference genome?

Download Human Reference Genome (HG19 – GRCh37)

  1. Download all (GZ) files – chromosomes. Create a directory that will store the downloaded files:
  2. Uncompress each GZ file – chromosome in the directory. Create a directory that will store the uncompressed files:
  3. Merge all chromosomes (1, 2, 3, …, X, Y) in one FASTA file.

How do I get sequence from UCSC Genome Browser?

Click the entry for the gene in the RefSeq or Known Genes track, then click the Genomic Sequence link. Alternatively, you can click the DNA link in the top menu bar of the Genome Browser tracks window to access options for displaying the sequence.

What is a chain file liftOver?

A liftOver file is a chain file, where for each region in the genome the alignments of the best/longest syntenic regions are used to translate features from one version of a genome to another.

What is hg38?

Yes, they are the same version of the human genome. GRCh Build 38 stands for “Genome Reference Consortium Human Reference 38” and it is the primary genome assembly in GenBank; hg38 is the ID used for GRCh Build 38 in the context of the UCSC Genome Browser.

How do I download UCSC tracks?

Downloading from a web browser If you are not comfortable using the command line, you can download your file via FTP in your browser at, or from our downloads page at

What is chain format?

The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense.

What are chain files?

To combine multiple files and view them as a single file, use Chain Files. For example, if you are translating or reviewing ten files with ten segments each, you can temporarily chain them into a single file of 100 segments. This is particularly useful with duplicate or similar content among files.

Is hg38 better than hg19?

Here, the improved reference genome (HG38) increased the number of SNVs identified from identical sequencing data, suggesting that genetic variants missed by using HG19 could be identified using HG38. Therefore, we again recommend the newer version (HG38) for sequencing data analysis aimed at variant calling.

What is the difference between hg18 and hg19?

if you are asking for the difference in the content, hg18 (or NCBI36, hg18 is just the UCSC’s nomenclature) is an older version of the human genome from ~2006, and hg19 (or GRCh37, hg19 is just UCSC’s nomenclature again) is the a newer one which I’m almost certain that it was first released on ~2009, although the …

Is hg19 the same as GRCh37?

In essence: GRCh37 is identical to hg19 on the main contigs (chr1-24), but differ on chrM.