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, 02:17, 20 September 2010
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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] | + | 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: |
| + | string name; "Name of gene" |
| + | string chrom; "Chromosome name" |
| + | char[1] strand; "+ or - for strand" |
| + | uint txStart; "Transcription start position" |
| + | uint txEnd; "Transcription end position" |
| + | uint cdsStart; "Coding region start" |
| + | uint cdsEnd; "Coding region end" |
| + | uint exonCount; "Number of exons" |
| + | uint[exonCount] exonStarts; "Exon start positions" |
| + | uint[exonCount] exonEnds; "Exon end positions" |
| + | |
| 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). |