Hi Paul, GRChr37.p5 refers to patch 5 of the GRCh37/hg19 assembly. Click on "show revision history" on NCBI's page for more details:
http://www.ncbi.nlm.nih.gov/genome/assembly/2758/ We display the GRChr37 version (without patches) in the Genome Browser. You can see the locations of the patches relative to GRChr37 by turning on the GRC Patch Release track (in the Mapping and Sequencing section). If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 4/20/12 9:49 AM, Paul Reynolds wrote: > To whom it may concern, > I just submitted a chromosomal coordinates file (Exons +/- 50 + > promoters) for a panel of 45 genes to the Ampliseq design tool. I have the > results. > When I take a primer and BLAST it, I find that the match is 10,000 nt > different from the input: BLAST match starts at 41166539 in chr 5, targeted > coordinates were 41176539. > The amplicons cover the targeted regions based on the coordinates > supplied by the UCSC Browser for GRHCh37/hg19. But I notice that the BLAST > match coordinates are given for GRChr37.p5. What is the difference between > /hg19 and .p5, and why is there a 10,000 nt difference? > > Thanks. > Paul Reynolds > Paul R Reynolds, PhD > Associate Professor > Department of Pediatrics > Neustadt Building, Room D311 > National Jewish Health > 1400 Jackson Street > Denver, CO 80206 > 303-398-1419 > Note new email: [email protected] > > > > NOTICE: This email message is for the sole use of the intended recipient(s) > and may contain confidential and privileged information. Any unauthorized > review, use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply email and destroy all > copies of the original message. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
