Here I want to show how to convert coordinates from mm10 to mm9 based on command line. 

And you also can do this using the web interface at http://genome.ucsc.edu/cgi-bin/hgLiftOver

The operating system in my computer is Ubuntu 18.10 (64-bit).

Liftover usage:

liftOver input.bed map.chain output.bed unlifted.bed

You need download two files from UCSC. The first one is “liftOver”, and the second one is ”map.chain”.

You can download “liftOver” from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/, and download ”map.chain”( mm10ToMm9.over.chain.gz) from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/liftOver/.

Then you can use the code listed above to convert the coordinate from mm10 to mm9

The code I used is showed below:

liftOver ./ElementFromGtf/gene.bed /media/chunjie/hd2/Software/liftOver/mm10ToMm9.over.chain ./ElementToMM9/gene.bed ./ElementToMM9/unlifted.gene.bed