lncRNA quantification featurecounts
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8 weeks ago
Beth • 0

Hi everyone, I want to analyze the differential expression of lncRNA using TCGA data processed with RSubread (FPKM and TPM, gene-level data, see here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804769/).

Is there any way to filter only lncRNA gene IDs from the output of featurecounts? And would it be relevant to use the values (counted with gene id) in the DE analysis of lncRNA?

Thank you in advance.

featurecounts TCGA lncRNA DE • 236 views
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Entering edit mode
8 weeks ago

I think you need at analyze everything together, then after you get your fold changes and p values, then you can look at the subset you care about.

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