Question: DE analysis of lncRNA from C elegans
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gravatar for Assa Yeroslaviz
13 months ago by
Assa Yeroslaviz1.2k
Munich
Assa Yeroslaviz1.2k wrote:

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

ADD COMMENTlink modified 13 months ago by swbarnes25.0k • written 13 months ago by Assa Yeroslaviz1.2k
0
gravatar for swbarnes2
13 months ago by
swbarnes25.0k
United States
swbarnes25.0k wrote:

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)

ADD COMMENTlink written 13 months ago by swbarnes25.0k

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)

ADD REPLYlink written 13 months ago by Assa Yeroslaviz1.2k
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