LiftOver

From Augix' Wiki

liftOver program is installed in:

/picb/home5/augix/bin/liftOver

Directly run it, you'll see the help information.

the program need you specify the following things: 1. -minMatch, minimal percentage of the matched part. 2. the file with coordinates in one species. I call it the oldFile, it's in BED format, check UCSC Genome Browser to understand more about BED format. 3. the chain file, this file contains the coordinate mapping information from one species to another. 4. the output file name, I call it the newFile.

Now it comes my bash code:

chain_h2c=/picb/compbio6/limingfeng/data/liftover/chain_file/hg18ToPanTro2.over.chain
chain_h2r=/picb/compbio6/limingfeng/data/liftover/chain_file/hg18ToRheMac2.over.chain
 
outdir=./0.8
if [ ! -d $outdir ]; then mkdir $outdir; fi
 
oldFile=../1.BED/human.promoter.bed
 
newFile=$outdir/chimp.promoter.bed
~/bin/liftOver -minMatch=0.80 $oldFile $chain_h2c $newFile unMapped
 
newFile=$outdir/rhesus.promoter.bed
~/bin/liftOver -minMatch=0.80 $oldFile $chain_h2r $newFile unMapped

I also provide an example of file in BED format.

$ head human.promoter.bed 
chr7	157955020	157956019	ENSG00000208234	0	+
chr17	15981912	15982911	ENSG00000199674	0	-
chr9	134883755	134884754	ENSG00000221622	0	+
chr6	52116106	52117105	ENSG00000207604	0	+
chr6	111436273	111437272	ENSG00000207431	0	-
chr6	65740007	65741006	ENSG00000221312	0	+
chr20	18187496	18188495	ENSG00000223135	0	-
chr5	29983692	29984691	ENSG00000223136	0	+
chr14	91340071	91341070	ENSG00000200159	0	-
chr9	108481079	108482078	ENSG00000200131	0	+

the columns are: chromosome name, start, end, gene id, score, strand. NOTICE: the liftOver program would not modify gene id and score, liftOver only converts chromosome name, start, end, and strand.