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, 02:36, 20 September 2010
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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" |
− | 2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the defination of "exonframe". For some genes, due to translational frame shifts or other reasons, the exonframe | + | 2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other reasons, the exonframe might not |
− | 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]. | + | match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is not a multiple of three". While we will use the usual mod 3 method for counting codons. |
− | 3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). | + | 3. 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]. |
| + | 4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570). |
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| Here is an example of input gene file headlines: | | Here is an example of input gene file headlines: |