Very high FPKM values (snoRNA) in RNAseq data

Question

[immunogirl2]

Recently I got RNA-seq data and found following kind of FPKM values in several samples for a "Small Nucleolar RNA" gene: FPKM value : 1.84E+08, 7.56E+07............

I think something went wrong (the library preparation, sequencing, and data analysis was performed by a commercial company). The experiment was whole-transcriptome analysis. I asked them what type of kit they used to cleanup RNA, and answer was "PolyA selection kit". Could snoRNA bind to OligodT beads? Can someone give me any clue so that I can handle this situation. Thanks in advance.

Answer 1

[Michael]

I think that a measurement of a single genomic sequence or feature does not constitute evidence, neither for nor against that something went wrong. No protocol is perfect and PolyA selection is still only an enrichment of polyadenylated sequences. I think you should get the raw data and run it through a standard QC and analysis pipeline. If the QC doesn't show anything unnormal and the rest of the transcripts is covered, who cares about one snoRNA?

[immunogirl2]

Thanks a lot. I'll make sure if QC and analysis is correct.