Question: chain files for mouse mm9 to ensembl version 75
0
gravatar for Saad Khan
4.1 years ago by
Saad Khan390
United States
Saad Khan390 wrote:

Hi,

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.

C: liftover chain files for mouse mm9 to ensembl version 75

thanks & regards

ADD COMMENTlink modified 4.1 years ago by Emily_Ensembl20k • written 4.1 years ago by Saad Khan390

Release 75 is GRCm38, so why not just liftOver to mm10 (i.e., GRCm38) and then convert the chromosome names?

ADD REPLYlink written 4.1 years ago by Devon Ryan94k

As I have highlighted in my earlier post I don't think it's as straightforward as just changing chromosome names. If I do it this way it won't be accurate. I was wondering if someone has done it using chain files and has already created a chain file for ucsc to ensembl mouse conversion which I can use.

ADD REPLYlink written 4.1 years ago by Saad Khan390

For GRCm38 it is in fact as straight forward as changing the chromosome names (with the possible exception of chrM/MT, since there were a couple releases where the sequences differ on those). I provide the name mappings here. The only things lacking in the UCSC reference are the patches.

ADD REPLYlink modified 6 weeks ago by RamRS25k • written 4.1 years ago by Devon Ryan94k

So correct me if I am wrong but ensembl uses 1-based coordinate system and UCSC uses 0-based coordinate system. So would I still need to change the coordinates after I have changed the chromosome names of the subsequent GRCm38 bed file?

ADD REPLYlink modified 6 weeks ago by RamRS25k • written 4.1 years ago by Saad Khan390

A BED file is always 0 based.

ADD REPLYlink written 4.1 years ago by Devon Ryan94k

Thanks Devon. Can you also please help me with this one.

Normalization scheme to use for upstream sequences read count in (Chip-seq histones)

regards

ADD REPLYlink modified 6 weeks ago by RamRS25k • written 4.1 years ago by Saad Khan390
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