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VcfCodingSnps

62 bytes added, 02:03, 13 December 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
1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 10 11 fields are required and must be of the same order as shown below:
string name; "Name of gene"
string chrom; "Chromosome name"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
string symbol; "Standard gene symbol"
Note:
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 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
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