Getting the number of Genes expressed in a sample
Hello Biostars Is it possible to get the information about the total number of genes expressed in one sample after RNAseq?
Thank you
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Sreeraj Thamban
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If you have done Cufflinks you could see genes.fpkm_tracking file to count the number of gene and isoforms.fpkm_tracking file to see total number of transcripts
Hi sreeraj, your question is somewhat profound. How would you define an expressed gene? - is an expressed gene any transcript that simply returns count values after data normalisation? If that is the case, then qudrat's answer is sufficient (if using Cufflinks).
Getting expression values for a single sample is absolutely no problem with any of the count abundance tools that I know. You just need to define a cut-off for expressed / not expressed and clearly state this.
One area where your question has much validity is in the determination of gene expression in different tissues. For example, many genes are 'ubiquitously' expressed across most tissues, whereas others are only expressed in certain organs/tissues.
Hello Kevin, I was interested in the third part of your answer. Is it possible to get that information after cufflinks?
Thank you
You mean that you are interested in tissue-specific expression? projects like FANTOM5 have open access data on this, but there are other more recent projects (that I cannot remember right now). You may want to open a new question on that particular topic (i.e. tissue-specific expression).
On the other hand, if you are interested in defining a cut-off for expressed / not expressed, there is no defined or standardised cut-off. For raw counts, which Cufflinks does not produce, people sometimes use 5 counts as the cut-off, whereas it can also be 10. You may want to check the distribution of your counts to see how it looks, and then decide what the cut-off could be. There is no standardised way to do this.