Hello, I am very interested in using the conservation data you published in the paper:
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005). The conservation data that I downloaded is from: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/phastCons30way/euarchontoglires/ Since in the paper you mentioned that the sequence data was downloaded from the UCSC repository, I downloaded the mm9 genome from: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/ When checking the data for chromosome 12 (mm9), I realized that its size (number of bases) is 121257550. The number of conservation predictions for chromosome 12 that I downloaded has only 88940836 bases. The header of the conservation file has something like: "fixedStep chrom=chr12 start=3000534 step=1" So even if I assume that the predictions start at position 3000534, the number of bases of the prediction and the ucsc chromosome 12 files do not match. Am I missing something? What would be the way of matching conservation predictions to the genome? or where can I download a genome sequence that matches the conservation dataset? Best regards, Arnoldo Jose Muller Molina Max-Planck-Institute for Molecular Biomedicine Computational Biology and Bioinformatics Group Röntgenstrasse 20 48149 Münster NRW, Germany _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
