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, 02:20, 20 September 2010
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| -s SNP file Specifies the name of input VCF-format SNP file | | -s SNP file Specifies the name of input VCF-format SNP file |
− | -g genefile Specifies the name of input gene file, by default use a gene list file (genelist.txt) in UCSC known gene format generated by UCSC genome browser | + | -g genefile Specifies the name of input gene file, by default use a NCBI36 version gene list file (genelist.txt) in UCSC known gene format generated by UCSC genome browser |
| -o output file Specifies the name of output VCF-format SNP file, by default will be named vcfCodingSNP.out.vcf | | -o output file Specifies the name of output VCF-format SNP file, by default will be named vcfCodingSNP.out.vcf |
| -r reference genome Specifies the name of reference genome file, by default will use NCBI build 36 reference genome | | -r reference genome Specifies the name of reference genome file, by default will use NCBI build 36 reference genome |
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| Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file | | Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file |
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− | 1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 fields are required and must be of the same order as shown below: | + | 1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 10 fields are required and must be of the same order as shown below: |
| string name; "Name of gene" | | string name; "Name of gene" |
| string chrom; "Chromosome name" | | string chrom; "Chromosome name" |
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| uint[exonCount] exonStarts; "Exon start positions" | | uint[exonCount] exonStarts; "Exon start positions" |
| uint[exonCount] exonEnds; "Exon end positions" | | uint[exonCount] exonEnds; "Exon end positions" |
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| 2. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables]. | | 2. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables]. |
| 3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). | | 3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). |