Using the location of lncRNA and find the up and downstream gene
I have some data about the location of the lncRNA (eg:chr1:83801516-83860546) , and I want find the lncRNA's up and downstream genome's name.
rna-seq
genome
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you should consider adding a bit more information in your question: eg. which genome? do you have to do this once or for several lncRNAs? The more you elaborate in your question the better (more useful) the answers will be.