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, 11:07, 7 June 2010
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| 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> |
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| + | == Sources of SQLite database tables == |
| + | |
| + | *[http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased HapMap phased haplotypes] |
| + | *[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 1000 Genomes phased haplotypes] |
| + | *[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP position] via the [http://genome.ucsc.edu UCSC Browser] |
| + | *[http://www.ncbi.nlm.nih.gov/RefSeq/ Gene and exon positions] via the [http://genome.ucsc.edu UCSC Browser]. We filtered SNPs that map to more than one location or where no allele matches the reference sequence |
| + | *[http://genome.usc.edu Annotation] We used various sources including RefSeq Genes (refFlat), TFBS Conserved (tfbsConsSites), and Conservation (phaseConsElements44wayPlacental) |
| + | *[ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03/pilot1 Recombination rates from HapMap] |
| + | |
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| == Input == | | == Input == |
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| <br> | | <br> |
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− | The file should be whitespace delimited, and the header (column names shown above) must exist. | + | The file should be whitespace delimited, and the header (column names shown above) must exist. |
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| == Output == | | == Output == |