Hello everyone,

I introduced a gene tagged with GFP to Arabidopsis, its expressing at both transcript and protein level and is showing the phenotype somewhat similar to what I expected.

Now i performed genome sequencing for the stable transgenic lines and want to know where actually is my gene integrated into Arabidopsis genome.

I guess mapping the reads to TAIR10 genome using TOPHAT and analyzing the unmapped reads (by blasting it to my gene of interest?), but i am not sure. 

Can anyone guide here? Thanks in advance :)

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