I'm using TopHat, cufflinks, etc. for the first time and 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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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...