DE analysis of lncRNA from C elegans

Question

[Assa Yeroslaviz]

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.

thanks Assa

Answer 1

[swbarnes2]

If the GTF used with STAR included the lincRNA features you want, I think you can just go ahead and use that. (Assuming that the library prep used was suitable for capturing lincRNA)

[Assa Yeroslaviz]

In the "normal" DE analysis results I have done with the STAR-featureCounts-DESeq2 workflow I have also got some of linc* genes I was referring to. But all except one are not differentially expressed in the conditions i am working with. Now I am not sure, whether this is a biological result or it is due to the wrong method I have used to analyse the data.

I know there are a lot of tools out there to analyse lncRNA either from RNA-Seq. So is there a reason why they exits? (I mean, if I can do the analysis just the same way I do RNA-Seq analysis)