Target genes of lncRNAs

Question

[Reza]

Dear all,

I have RNA seq data from different tissues of one plant with the reference genome. I am trying to find out target genes of lncRNAs as cis-acting target genes. How can I identify and separate the target genes within 100 kb upstream or downstream of lncRNAs? Are there any codes or packages to let me get all target genes?

Thanks!