Hi, I'm attempting to reproduce the phastCons most conserved elements tract for placental mammals from the multiz-28way alignments. I've initially attempted to do this just for chromosome 1, and whilst there is fairly good agreement, I'm getting some differences.
The phastCons command I've used is: phastCons -i MAF -n -s -E 45 -C 0.3 -R 0.31 --not-informative panTro2,rheMac2 -V chr1.bed multiz28way/maf/chr1.maf placental.mod where placental.mod is taken from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons28way/placental.mod and is as follows ALPHABET: A C G T ORDER: 0 SUBST_MOD: REV BACKGROUND: 0.295000 0.205000 0.205000 0.295000 RATE_MAT: -0.990634 0.178819 0.490738 0.321078 0.257325 -1.001677 0.186563 0.557790 0.706184 0.186563 -1.161873 0.269126 0.321078 0.387615 0.187019 -0.895713 TREE: (((((((hg18:0.005873,panTro2:0.007668):0.026074,rheMac2:0.031973):0.073300,otoGar1:0.151185):0.015682,tupBel1:0.162844):0.006272,(((rn4:0.084383,mm8:0.076274):0.200607,cavPor2:0.202990):0.034350,oryCun1:0.208548):0.014587):0.019763,((sorAra1:0.248532,eriEur1:0.222255):0.045693,(((canFam2:0.101137,felCat3:0.098203):0.048213,equCab1:0.099323):0.007287,bosTau3:0.163945):0.012398):0.018928):0.030081,(dasNov1:0.133274,(loxAfr1:0.103030,echTel1:0.232706):0.049511):0.008424); The majority of elements have identical coordinates, although a large number differ by a single base (and in these cases the predicted conserved elements that I download from the UCSC genome browser start 1bp before the conserved elements I find using the above command). Furthermore, the predicted conserved elements I obtain contain a single very large element amongst the other predictions which has a very low (and negative) score. In BED format, this element is: chr1 120376987 247198473 chr1.105012 -999999999 + I'm not sure why I am observing these differences, but I would be very grateful if you could help explain what might be going on. Many thanks, Dan Halligan -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
