CpG coordinates information

Question

[elias01cj]

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!!

Elías

Answer 1

[cmdcolin]

it's a little unclear what your question is but you can export the UCSC data about CpG including their coordinates and "percent CpG"

the get output of the entire cpgIslandExt table looks like

#bin    chrom   chromStart  chromEnd    name    length  cpgNum  gcNum   perCpg  perGc   obsExp
27  chr1    155188536   155192004   CpG: 361    3468    361 2761    20.8    79.6    0.73
...

so chrom, chromStart, chromEnd tells you the position, and perCpg tells you percent CpG in the island

[elias01cj]

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!

[cmdcolin]

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?

[elias01cj]

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.