Hey all, I have a more scientific question in nature. Essentially, my group has done meta-transcriptomics for the first time in our lab and we encountered some issues with extraction. Under the guidance of the sequencing facility we then used a whole lane to sequence everything (no rRNA depletion) and recieved ~ 40million reads per sample. Assuming we have 90% rRNA we'll end up with ~4million reads. Is this enough for differential expression analysis? Has this type of analysis been done on communities with this low level of sequencing in the past? I'm trying to find technical validity in moving forward, as well as trying to learn what limitations analysis wise we should be concerned about. Any help, references, discussion, etc. would be greatly appreciated!
If you are working with a synthetic community composed by few strains, 4 million reads are not great not terrible.
With natural community however, you will probably get some (differential expressed?) transcripts representing highly transcribed genes from the most abundant and transcriptionally active microbes. How much informative this could be? it totally depends on what are you looking for.
This is a natural community derived from marine sampling. One of our main ideas was to look at differentially expressed transcripts for specific metabolisms. So in essence, we may be able to determine some active pathways in the most abundant microbes with these data?
If the community isn't to complex, yes... but keep your expectations low