Entering edit mode
4 weeks ago
elias01cj
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0
Hi,
I know that it is possible to get the coordinates about CpG islands in the genome at UCSC (https://genome.ucsc.edu/cgi-bin/hgTables), but some islands only have 10% of CpG sites on them. Does anyone know if it's possible to get the coordinates for the different CpG sites?
Thanks!!
ElĂas
Sorry. I meant that I knew the coordinates for the CpG islands were available, but is it possible to get the coordinates for the individual CpG sites within the islands?
Thank you!
gotcha. i am not sure if that is available as any readily downloadable data file. i would consider writing a script to combine e.g. the reference genome fasta and the UCSC data to do such a thing (e.g. just find the letters "CG", corresponding to the CpG on the forward strand, or "GC", corresponding to the CpG on the reverse strand, in the region). is there a particular reason you want this information?
Thanks! I was looking for the file but couldn't find anything, so I came here to ask. I followed your advice and created the file myself. I need it to run this tool: https://github.com/epifluidlab/FinaleMe, which requires the CpG coordinates.