Hi all, I was wondering how to do a differential expression analysis of long non-coding RNA (lncRNA) from my data set of C elegans samples. We have multiple samples from four different conditions. The raw data came from total-RNA. We have done already RNA-Seq analysis on the samples and woule like now to analyse the DE of lncRNAs in the data.
I was wondering how to do this. The tools I have found online so far are all for human or mouse, but no C. elegans. Is there a special way to do the analysis?
The raw files were already mapped to the C. elegans genome using STAR and the quantification was done using featureCounts for the RNA-Seq DE analysis. Can i use the results from this analysis for the lncRNA-Seq DE analysis?
I have downloaded a list of ncRNA/lincRNA genes from the ensembl biomart repository. Unfortunately I am not sure how to integrate this information into the analysis.
I would appreciate the help or advices regarding on how to proceed.