This a a package designed for trangenic integration and rearrangement sites discovery using sequencing data
TransgeneR uses bowtie2 as the alignment tool. Therefore, before usage, bowtie2 must have been installed in the linux mechine and its location has been added to $PATH variable. Meanwhile, the genome reference index has been constructed using "bowtie2-build" command.
#The whole analysis can be done using transgeneR function.
test.data=system.file("extdata", "test.zip", package = "transgeneR") temp <- tempdir() unzip(test.data, exdir=temp) output.dir=paste(temp,"/test",sep="") transgene.sq=paste(temp,"/test/temp_files/insert.fa",sep="") transgeneR(output.dir, insert.seq=transgene.sq)
#If WGS is used and the sequencing depth is > 30, you can do copy number estimation using "fragment.estimation".
?fragment.estimation fragment.estimation(output.dir, min.counts=3)
Q & A
error: /usr/bin/ld: cannot find -lboost_iostreams
Please install boost library in your system using the command like:
yum install boost-devel
Who to contact for any issues？
Please send email to email@example.com
How to cite?