Dear UCSC GenomeBrowser staff: I wanted to map probe sequences from U133plus2 chip to human genome.
I downloaded all chromosomes in FASTA format from ncbi FTP site: For example: hs_ref_GRCh37_chrX.fa.gz I used BLAST to map the probe sequence to fasta file mentioned above. I used strict conditions that I wanted only 100% identical hit. One such probe hit: probe:HG-U133_Plus_2:208763_s_at:318:797 Homo sapiens chromosome X genomic contig, GRCh37 reference primary assembly 25 25 1 30253299 30253323 when I try to find chrX:30253299-30253323, the position does not map to the location it should have pointed. the desired position is : 000000001 gggagtattgactggtcccttacct 000000025 <<<<<<<<< ||||||||||||||||||||||||| <<<<<<<<< 106957015 gggagtattgactggtcccttacct 106956991 My question: Although NCBI and UCSC are same reference genomes, why am I having different position. Is this because I am searching against a contig as opposed to a full chromosome. Please help me. thanks Adrian _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
