The availability of T-DNA insertion sites is very important for functional genomics research and the screening and identification of transgenic. However, the present protocols for identifying T-DNA insertion sites, like reverse PCR and semi-random primer PCR, are not only complex and time-consuming, but also inefficient. In this GitHub, T-DNA_Insertion_Identify.sh established a simple, reliable and efficient method for obtaining T-DNA insertion sites in transgenic.
Academic users may download and use the application free of charge according to the accompanying license.
Commercial users must obtain a commercial license from Xukai Li.
Put T-DNA_Insertion_Identify.sh and all Fastq files and T-DNA.fa genome.fa in a same dir, then run:
sh T-DNA_Insertion_Identify.sh T-DNA.fa genome.faAnd the results in CandiT-DNA.T-DNA.txt file are like this:
#Chr Breakpoint_Start Breakpoint_End Break_Length
Chr1 Start: 5251250 End: 5251267 Length: 17
Then use IGV to see the sam and ref.fa files and check T-DNA Insertion Loci.
For any questions please contact xukai_li@sxau.edu.cn or xukai_li@qq.com