Hello, I've noticed an inexplicably large difference between the D.melanogaster 15-way phastcons data available for download in the fixed step format (in particular, http://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/chr2L.pp.gz) and the same in the variableStep format accessible from the Tables view for the same D.melanogaster assembly.
They do look very similar at the beginning of the chromosome, as expected, - for example here are the first 20: pos_on_chr2L variableStep fixedStep 1 0.770953 0.771 2 0.77874 0.78 3 0.770953 0.772 4 0.77874 0.785 5 0.77874 0.78 6 0.755378 0.761 7 0.716441 0.722 8 0.708654 0.71 9 0.708654 0.716 10 0.700866 0.703 11 0.708654 0.712 12 0.700866 0.701 13 0.661929 0.667 14 0.59963 0.604 15 0.475031 0.479 16 0.264772 0.27 17 0.140173 0.146 18 0.132386 0.138 19 0.101236 0.109 20 0.101236 0.103 But by as early as 5400 they already look completely out of sync: pos_on_chr2L variableStep fixedStep 5400 0.958661 0.251 5401 0.966331 0.345 5402 0.966331 0.383 5403 0.966331 0.39 5404 0.950992 0.376 5405 0.935654 0.229 5406 0.904976 0.211 5407 0.851291 0.166 5408 0.743921 0.152 5409 0.690236 0.116 5410 0.582866 0.044 5411 0.575197 0.017 5412 0.552189 0.019 5413 0.490835 0.017 5414 0.368126 0.01 5415 0.368126 0.018 5416 0.345118 0.022 5417 0.291433 0.039 5418 0.184063 0.05 5419 0.130378 0.054 5420 0.10737 0.054 This goes well beyond the listed loss of resolution for this fragment (Worst case: 0.00760937). >From some functional tests it seems that the variableStep data makes more sense - although I've got not solid proof. Can you please look into this - maybe I'm just confusing something? Many thanks Mikhail -- Mikhail Spivakov, PhD Postdoctoral Fellow EMBL-EBI Hinxton Cambridge CB10 1SD UK _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
