Dear UCSC Genome Browser Personnel, When I use the Table Browser with the following specs...
Clade: Mammal Genome: Human Assembly: hg18 Group: Denisova Assembly and Analysis Track: Denisova Table: bamSLDenisova Define Regions: chr16:10,019,760-10,019,760 (for example) Intersection: group: Variants and Repeats-track: SNPs130-Table_SNPs130 Output format: sequence Output type returned: plain text ...the output I get contains the allele of the reference human (A) as opposed to the C which is visible when using the visual browser itself. When I removed the intersection and simply attempted to get the output as "Sequence the sequence which is given to me (see below) has the reference human allele at the position in question (chr16: 10019760). All of my results I am getting where the Denisova differs from the Reference Human have this same problem. Am I doing something wrong? I am just trying to get the Denisova allele at the various SNP130 snps at the positions I am entering, so could you please advise me? >hg18_bamSLDenisova_C_M_SOLEXA-GA04_PE_JK_3003_3004:5:35:10988:4706#GTCGACT >range=chr16:10019706-10019765 5'pad=0 3'pad=0 strand=+ repeatMasking=none AAGAAGGTGGGGTTTCTGTGCTAGCACCAGAAGACACAAACTGGAGGCAG CAATACCACT >hg18_bamSLDenisova_C_M_SOLEXA-GA01_PEi_JK_3003:3:116:17181:9520#GTCGACT >range=chr16:10019727-10019786 5'pad=0 3'pad=0 strand=+ repeatMasking=none TAGCACCAGAAGACACAAACTGGAGGCAGCAATACCACTGCAGTTGATGT GACAGAAGCC Sincerely, Rob Lowery _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
