I have a bed file of mapped reads (mapped to mm9) and I need to convert coordinates of bed file mapped to ucsc mouse assembly to ensembl mouse assembly.
One way to possibly do that is to convert it using chain files (chain files to be used with crossmap (http://crossmap.sourceforge.net/)).
Unfortunately the chain files for converting mouse (mm9) coordinates to corresponding ensembl version 75 coordinates is not available (AFAIK). Since it is a common problem encountered I was wondering if someone has already done it and the chain files are available somewhere on the web. I would be grateful if someone could point me to them.
I had treid asking this question earlier bit it seems my question was misunderstood. I tried clarifying by message but did not get any response so I am posting the link to that question here again.
thanks & regards