chainNetSyntenic

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Description

Wrapper function of chainNetSyntenic: Makes alignment nets out of chains and adds synteny info to net. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platforms.

Usage

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  chainNetSyntenic(allPreChain, assemblyTarget, assemblyQuery,
                   netSyntenicFile=paste0(sub("\\.2bit$", "",
                                              basename(assemblyTarget),
                                              ignore.case = TRUE), ".",
                                          sub("\\.2bit$", "",
                                              basename(assemblyQuery),
                                              ignore.case = TRUE),
                                              ".noClass.net"),
                   binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic")

Arguments

allPreChain

character(1): file names of input allPreChain file.

assemblyTarget

character(1): the file name of target assembly twoBit file.

assemblyQuery

character(1): the file name of query assembly twoBit file.

netSyntenicFile

character(1): file names of output netSyntenicFile file.

binaryChainNet

character(1): the name/filename of the binary chainNet to call.

binaryNetSyntenic

character(1): the name/filename of the binary netSyntenic to call.

Details

Add classification information using the database tables: actually this step is not necessary in this pipeline according to http://blog.gmane.org/gmane.science.biology.ucscgenome.general/month=20130301. The class information will only be used for Genome Browser. Since it needs some specific modification of the table names for certain species, we skip this step now. If this step is done, then the generated class.net is the gzipped net file that you see in UCSC Downloads area.

Value

character(1): the file names of generated net file.

Author(s)

Ge Tan

References

http://hgdownload.cse.ucsc.edu/admin/exe/

See Also

chainPreNet

Examples

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  ## Not run: 
  ## This example doesn't run because it requires two bit files and external
  ## Kent utilities.
    allPreChain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                             "danRer10.hg38.all.pre.chain")
    assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
    assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
    chainNetSyntenic(allPreChain, assemblyTarget, assemblyQuery,
                     netSyntenicFile=file.path(
                       "/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                                               paste0(sub("\\.2bit$", "",
                                                      basename(assemblyTarget),
                                                      ignore.case = TRUE), ".",
                                                      sub("\\.2bit$", "",
                                                      basename(assemblyQuery),
                                                      ignore.case = TRUE),
                                              ".noClass.net")),
                     binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic")
  
## End(Not run)

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