This script will convert bigwig files from coordinates hg18 to coordinates hg19 of the human genome.
Script:
- checks if bigwigToBedGraph is present if not downloads it
- converts the bigwig to bedgraph using bigwigToBedGraph
- checks if liftOver is present if not downloads it
- lifts over the bedgraph preserving the fourth column using -bedPlus=4
- sorts the liftover output bedgraph file
- downloads hg19.chrom.sizes for bedGraphToBigWig
- checks if bedGraphToBigWig is present if not downloads it
- converts the bedgraph back to bigwig using bedGraphToBigWig
Script will save new bigwig file with .hg19 extension
#Usage
chmod 755 ./bigWigLiftOver.sh ./bigWigLiftOver.sh path/to/bigwig/file.bw
#Example
mpjanic@valkyr:~$ ./bigWigLiftOver.sh out.bw Proccesing file: /home/mpjanic/out.bw --2017-03-13 14:52:34-- http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bigWigToBedGraph Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1138396 (1.1M) [text/plain] Saving to: ‘bigWigToBedGraph’ 100%[=======================================================================================================================================================>] 1,138,396 --.-K/s in 0.03s 2017-03-13 14:52:34 (33.4 MB/s) - ‘bigWigToBedGraph’ saved [1138396/1138396] --2017-03-13 14:52:50-- http://hgdownload.cse.ucsc.edu/goldenpath/hg18/liftOver/hg18ToHg19.over.chain.gz Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 140346 (137K) [application/x-gzip] Saving to: ‘hg18ToHg19.over.chain.gz’ 100%[=======================================================================================================================================================>] 140,346 --.-K/s in 0.009s 2017-03-13 14:52:50 (15.5 MB/s) - ‘hg18ToHg19.over.chain.gz’ saved [140346/140346] --2017-03-13 14:52:50-- http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/liftOver Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 8618486 (8.2M) [text/plain] Saving to: ‘liftOver’ 100%[=======================================================================================================================================================>] 8,618,486 47.4MB/s in 0.2s 2017-03-13 14:52:51 (47.4 MB/s) - ‘liftOver’ saved [8618486/8618486] Reading liftover chains Mapping coordinates --2017-03-13 14:53:45-- https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes Resolving genome.ucsc.edu (genome.ucsc.edu)... 128.114.119.132, 128.114.119.133, 128.114.119.131, ... Connecting to genome.ucsc.edu (genome.ucsc.edu)|128.114.119.132|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1971 (1.9K) [text/plain] Saving to: ‘hg19.chrom.sizes’ 100%[=======================================================================================================================================================>] 1,971 --.-K/s in 0s 2017-03-13 14:53:45 (45.8 MB/s) - ‘hg19.chrom.sizes’ saved [1971/1971] --2017-03-13 14:53:45-- http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bedGraphToBigWig Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1148287 (1.1M) [text/plain] Saving to: ‘bedGraphToBigWig’ 100%[=======================================================================================================================================================>] 1,148,287 --.-K/s in 0.03s 2017-03-13 14:53:45 (34.0 MB/s) - ‘bedGraphToBigWig’ saved [1148287/1148287]