Hg38 Mapping Track Settings
 
Hg38 Mappings: UCSC LiftOver and NCBI ReMap   (All Mapping and Sequencing tracks)

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 UCSC liftOver to hg38  UCSC liftOver alignments to hg38   Schema 
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 NCBI ReMap hg38  NCBI ReMap alignments to hg38/GRCh38   Schema 
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 ReMap + axtChain hg38  NCBI ReMap alignments to hg38/GRCh38, joined by axtChain   Schema 

Description

This track shows alignments from the hg19 to the hg38 genome assembly, used by the UCSC liftOver tool and NCBI's ReMap service, respectively.

Display Conventions and Configuration

The track has three subtracks, one for UCSC and two for NCBI alignments.

The alignments are shown as "chains" of alignable regions. The display is similar to the other chain tracks, see our chain display documentation for more information.

Data access

UCSC liftOver chain files for hg19 to hg38 can be obtained from a dedicated directory on our Download server. The NCBI chain file can be obtained from the MySQL tables directory on our download server, the filename is 'chainHg38ReMap.txt.gz'.

Both tables can also be explored interactively with the Table Browser or the Data Integrator.

Methods

ReMap 2.2 alignments were downloaded from the NCBI FTP site and converted with the UCSC kent command line tools. Like all data processing for the genome browser, the procedure is documented in our hg19 makeDoc file.

Credits

Thanks to NCBI for making the ReMap data available and to Angie Hinrichs for the file conversion.