I am interested in finding non-coding RNA (lncRNA, eRNA) that are being differentially expressed in the disease case. For genes, doing this is pretty easy with DESeq2. But a collaborator told me that DESeq2 couldn't be used right away for the non-coding transcripts.
Is this true? What are some of the things that I should keep in mind while analyzing non-coding transcripts using DESeq2? He had mentioned that since the amount of ncRNA varies from sample to sample, special care has to be taken to normalize for that. The samples were depleted for ribosomal RNA, but he said that there would still be a lot of rRNA in the samples, and this amount differs from one sample to another.
The data are from total-RNAseq.