Hi Genome browser officers, I have a question about the consistency of coordinates across different tables in UCSC genome browser. Do all the tables in UCSC genome browser Human Assembly H19 has the same coordinate system? The reason why I ask this question is that right now, I want to extract all SNPs located in promoter regionsof some genes. I used table "RefGene" rather than "UCSCKnownGene" as the coordinates to defined the promoter regions.Then I used "allSnp132" table to get the coordinates for SNPs. Then I to see what SNPs with coordinates within region of promoter according to coordinate of "RefGene" rather than "UcscKnownGene". Is this okey? Are all tables and databases in UCSC genome browser human Hg19 based on GRCh37 assembly? Also, does the tables in ENCODE project also have the same coordinate system as GRCh37 assembly cause I am also interested to intersect some SNPs according to ENCODE project? Thank you very much!
Best regards, Yiyi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
