Question: Mapping Recombination Rate Coordinates To Ensembl Gene Features...
1
gravatar for Steve Moss
6.3 years ago by
Steve Moss2.2k
United Kingdom
Steve Moss2.2k wrote:

I'm hoping to do some analyses for the final stages of my PhD, looking at whether there are correlations between particular gene features and recombination rates across the genome. I was hoping to do a comparative analyses across species, but of course this depends on the existence of recombination rate data for those species (ReDB has data for some, but it seems to be very old). The latest data for human is available here http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/latest/rates/ and takes the following format:

position COMBINED_rate(cM/Mb) Genetic_Map(cM)
72434 0.0015000000 0
78032 0.0015000000 0.0000083970
554461 0.0015000000 0.0007230405
554484 0.0015000000 0.0007230750
555296 0.0015000000 0.0007242930
558185 0.0015000000 0.0007286265
558390 0.0010000000 0.0007289340

The genomic positions in these data are based on NCBI36 according to the README, however I have been using EnsEMBL and had planned to use the release 69 annotations, which are based on GRCh37. The last EnsEMBL release based on NCBI36 was release 54. I found this tool however http://www.ensembl.org/Homo_sapiens/UserData/SelectFeatures?db=core, which may be useful?

I have had a read of the following posts (Taking Hapmap Data To The Latest Genome Build and How Do You Manage Moving Existing Projects To A New Genome Build?), which seem relevant, but focus more on mapping HapMap SNP data rather than recombination rate, though I can imagine the methods are relatively similar. EnsEMBL pulls in HapMap and other SNP data into it's variation database, but no recombination rate data as far as I can tell, so it isn't going to be as easy as an API call.

From what I can tell I am going to need to locate recombination maps for individual species and convert coordinates to EnsEMBL's GRCh37 based data. Might not be as simple as I had first hoped :S

My questions are:

  1. Is anyone aware of an up-to-date genome-wide recombination rate data source for multiple species?
  2. How can I best convert coordinates between different releases so I can map RR to gene features?
ADD COMMENTlink modified 6.3 years ago by Pierre Lindenbaum118k • written 6.3 years ago by Steve Moss2.2k
1
gravatar for Pierre Lindenbaum
6.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

For "How can I best convert coordinates between different releases so I can map RR to gene features?", you could use the answers of:

How to convert centimorgan to base pair

ADD COMMENTlink written 6.3 years ago by Pierre Lindenbaum118k

Thanks for the answer Pierre, will take a look at that :)

ADD REPLYlink written 6.3 years ago by Steve Moss2.2k
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