Hi Yiyi, Yes, all tables on a particular assembly, including ENCODE tables, share the same coordinate system, and UCSC hg19 is synonymous with GRCh37. So, all tables in the GRCh37/hg19 assembly use the same coordinates. The tables in the hg18 assembly (or any other assembly) have different coordinates.
If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/22/11 11:39 AM, Ma, Yiyi wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
