Hello Gentlepeople, I have been working with the knownGene table and I am confused about some of the rows in this table. Here, I'll submit an exceptionally confusing entry from the table. It was exported as bed format file:
['chr1', '149397113', '149399229', 'uc010pbi.1', '0', '-', '149397113', '149397113', '0', '1', '2116,', '0,'] According to the bed file format we know that the fields represent the following values: chromosome, chromStart, chromEnd, name, score, strand, thickStart (start codon), thickEnd (stop codon), itemRgb, blockCount (number of exons), blockSizes (exon sizes), blockStarts (exons starts) My confusion has arisen from the fact that thickStart == thickEnd. This would mean that the start and stop codon are one and the same? Also confusing is that blockCount == 1. How can there be an exon if the start and end codon are at the same spot? In fact, the blockSizes field indicates that the exon is 2116 bases long. How can this be? Am I misinterpreting these values? What am I missing? If this is not the right forum to ask this question then can you guide me to a suitable resource? TIA, Lionel "Lee" Brooks 3rd Dartmouth Genetics Graduate Student _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
