Dear group members, I have several questions I am trying to get help with:
step 5 in this message (https://lists.soe.ucsc.edu/pipermail/genome/2006-February/009806.html) says "5. Go back up to group: and change it to "Comparative Genomics", track: Conservation, table: multiz8way." All is good except under table header I see three options: 1) Mammal Cons (phylo44wayPlacMammal) 2) Mammal Cons (phastCons44wayPlacentak) and 3) Mammal El (phastConsElements44wayPlacental) I am trying to find conservation score for some human SNPs. Which one would be the best? ------------------ I have a BED file of my SNPs (only 4 columns: chr, start, end, name) that I would like to intersect with one of the phastCons files above to get conservation scores for my SNPs. Can someone provide me with step-by-step instructions? ------------ Is there a way I can see conservation score of a single SNP on UCSC genome browser just to be sure I am getting correct scores if I successfully download the scores using intersecting tables? ------------- I am trying to find proximity of my SNPs to CpG islands. Can someone provide me with instructions on how to upload my list of files and get the proximity. Sorry that I just a beginner so step-by-step instructions would be very helpful. I hope these are not too much to ask. Thank you very much for all the great help. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
