We plan to perform RNAseq from whole transcriptome from FFPE tissue with 50 to 100 million paired-end reads mainly for DE analysis. The extracted RNA will be enriched by ribosomal RNA depletion and will yield degraded total RNA with RIN in the range of 2 to 3. Our question is: Which read length in the range from 50 to 300 bases you think is producing the best statistical reliable and biological meaningful results, considering that this kind of degraded RNA has an increased population of shorter fragments versus a lower population of longer fragments compared to non-degraded RNA. Does this kind of fragment distribution rather make results from shorter read lengths (e.g. 50b) more statistical valid, than performing longer reads (e.g. 150b) from very low fragment populations? Or doesn't this matter at all, since for shotgun sequencing the fragment lengths of degraded RNA with RIN 2 to 3 is still good enough to perform even longer reads?
Question: Best statistical validity for RNAseq from FFPE samples at different read lengths
2.0 years ago by
achimbell • 0
achimbell • 0 wrote:
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