Question: Liftover Of Na12878 Coordinates Into Hg19 Coordinates
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gravatar for Geparada
5.8 years ago by
Geparada1.3k
Cambridge
Geparada1.3k wrote:

Hi!!

I generated a NA12878 alternate genome file NA12878/hg18 VCF file and the hg18 assembly available on 1000 Genomes ftp server using GATK tools. Now I'll map RNA-seq reads to this genome and generate a BED12 file with the regions of my interest.

In order to compare this results with my previous work, I need to transform the BED12 coordinates, based on the NA12378 genome, into hg19 coordinates.

Can you suggest me a good way to this?

Thanks for your time!!

vcf bed liftover • 1.7k views
ADD COMMENTlink written 5.8 years ago by Geparada1.3k

Detailed post on tools for converting genome coordinates between builds: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

ADD REPLYlink written 10 weeks ago by Malachi Griffith16k
1
gravatar for Pierre Lindenbaum
5.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum100k wrote:

use the liftOver binaries: http://hgdownload.cse.ucsc.edu/admin/exe/ and the associated files: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/

ADD COMMENTlink written 5.8 years ago by Pierre Lindenbaum100k
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