transgeneR

This a a package designed for trangenic integration and rearrangement sites discovery using sequencing data

Install TransgeneR

library(devtools)

install_github("menggf/transgeneR")

prerequisite

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.

usage

#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

1. error: /usr/bin/ld: cannot find -lboost_iostreams

   Please install boost library in your system using the command like:

   yum install boost-devel

2. Who to contact for any issues？

   Please send email to menggf@gmail.com

3. How to cite?

   https://www.biorxiv.org/content/10.1101/462267v1