I'm using TopHat, cufflinks, etc. for the first time. I am analyzing two small RNAseq datasets, one of which is derived from a RNAi knockdown of a human gene. I tried looking for the relevant gene in the cuffdiff output to validate the experiment and the analysis. For some reason, the gene is not listed (nor are any genomic loci near it). Problem is, I know there were several reads from this gene in both control and knockdown datasets. Am I misunderstanding how TopHat, cufflinks, etc. work and reports results? To me, it looks like the report should contain all hits regardless of whether a significant difference was found or not.
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Last edited by drdna; 05-10-2012, 11:15 AM.
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