Hello Jing, Thank you for pointing this out - I'll forward on the request to make this clearer on the Phylo-P downloads README file.
http://genome.ucsc.edu/goldenPath/help/wiggle.html The data is in wiggle format, so the coordinates are 1-based. excerpt from wiggle.html --- Data Values Wiggle track data values can be integer or real, positive or negative values. Chromosome positions are specified as 1-relative. For a chromosome of length N, the first position is 1 and the last position is N. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data must be in numerical order. --- Thank you again and please let us know if you would like more assistance by contacting the mailing list again anytime. Best, Jen UCSC Genome Browser Support On 8/31/10 11:20 AM, jing zhang wrote: > Hello, > > This is Jing from USC, and currently I am trying to use the PhyloP > conservation score data in UCSC genome browser. I am confused by the > coordinates there. In table descriptions for both PhastCons and PhyloP, the > starting positions are all mentioned as 0 based. However, in the PhastCons > file format description, the starting positions are specifically pointed out > at 1 based, while there is no such explanation for the PhyloP file. However, > since the PhyloP file as stored in the same format as the PhastCons, I am > not sure about the coordinates are 1 based or 0 based. Would you please give > me some suggestions on this? Thank you very much for your help. > > Best Regards, > Jing > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
