how to do make differential expression of lncRNA from RNA-seq data
I have the data of RNA-seq in three periods. In this paper, the differential expression of mRNA and lncRNA in two periods was analyzed respectively. if i do this, what sholud i do
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Could you please provide us a link to "this paper", perhaps?
Dynamic expression of long noncoding RNAs reveals their potential roles in spermatogenesis and fertility
You just can do a standard RNASeq data and differential expression analysis. There is one peculiarity though with lncRNAs - when doing DE analysis, you should analyze them using the read counts of all genes (not only lncRNAs). Look here https://academic.oup.com/gigascience/article/8/12/giz145/5663671?login=true and here https://www.mdpi.com/2072-6694/12/10/2844/htm#B76-cancers-12-02844