liftover chain files for mouse mm9 to ensembl version 75

Question

[Saad Khan]

Hi,

I have a bed file of mapped reads (mapped to mm9) and I need to convert mm9 to Grcm38 (ensemble version 75) format. I was wondering if there is a liftover chain file already available to do that and if someone can point me to that. Since the chain file creation steps in the wiki (http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver) are not well documented and take longer for large genomes like that of mouse I was wondering if someone has already tried that and has a script or workflow with the right set of paramers to do that.

regards

Answer 1

[Sukhi Singh]

I think you need to convert first mm9 -> Grcm37 (hg19) then Grcm37 (hg19) -> Grcm38 (hg38)

Also, the chain files are available to download, you don't need to construct one for most of the cases.

For small conversions, you can also use the web-interface.

Answer 2

[Emily]

Here is the assembly converter and here are the mouse chain files. You definitely do not need to convert anything via human like Sukhdeep is saying.

[Sukhi Singh]

Thanks for the correction Emily, the interface link I added from UCSC genome browser, doesn't allow the straight conversion, that's why I suggested it might be the case.

[Saad Khan]

I think there has been a misunderstanding. I am not converting anything via human and the chain files that are available on UCSC are only UCSC specific. I am trying to make a chain file between corresponding versions of mouse genome in ensembl and ucsc (mm9 in particular). Grcm38 is not human (it is GRch38) GRcm38 is mouse genome of ensembl version 75/83. There are subtle differences between ensembl and ucsc genome and its not as straightforward as adding/removing chr prefix as some people sometimes do. Thus I was wondering if the chain files are already available and what are the parameters w.r.t generating these chain files for blat in particular as the "minimal steps" command takes too long.

PS: Tools like crossmap can convert the bed/gtf/gff/bam files between different assemblies but they require a chain file for that. A chain file for hg19 to GRch37 is already available on crossmap website. I am looking for the same in Mouse if somebody has it. http://sourceforge.net/projects/crossmap/files/chain_files/hg19ToGRCh37.over.chain.gz/download