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From Genome Analysis Wiki
Jump to navigationJump to search→Step 4: Install LocusZoom
*the LocusZoom python application
*the LocusZoom python application
*the R script used for generating plots
*the R script used for generating plots
*UCSC human genome '''build hg18''' data, including:
*Human genome '''build hg18''' data, including:
**genotype files (used for computing LD) from hapmap and 1000G
**genotype files (used for computing LD) from HapMap and 1000G
**a SQLite database file containing tables describing SNP positions, SNP annotations, gene and exon locations, and recombination rates
**a SQLite database file containing tables describing SNP positions, SNP annotations, gene and exon locations, and recombination rates
It is important that this directory structure remain intact. To make launching locusoom easier, you could create a link to it from /usr/local/bin, for example:
It is important that this directory structure remain intact. To make launching locusoom easier, you could create a link to it from /usr/local/bin, for example:
<pre>ln -s bin/locuszoom /usr/local/bin/locuszoom</pre>
<pre>ln -s bin/locuszoom /usr/local/bin/locuszoom</pre>
Sources of SQLite database tables;
HapMap phased haplotypes: http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased/
1000G phased haplotypes: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1/
SNP position: http://genome.ucsc.edu
SNP annotation for 1000G SNPs: Custom-designed by Peter Chines (pchines@mail.nih.gov)
Gene and exon positions: http://genome.ucsc.edu
Recombination rates from HapMap: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1/
== Input ==
== Input ==
