I'm working with Ribo-Seq in mouse and I would like to know if someone with experience could tell me how deep in number of reads is enough per sample?
Thank's.
5-10 million non-rRNA fragments are sufficient to detect all but a few of the most low expressed genes in diverse bacteria growing under a variety of conditions.
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-734
Also, check this out:
http://www.readcube.com/articles/10.1038/nrg3642
I agree with Deepak. In addition, it is important that you consider the complexity of the sequencing sample, i.e. how many different reads there are in your sequencing reads. See e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351865/, section "Considerations in NGSlibrary preparation: Complexity, bias, and batch effects". However, all depends of what you want to do with the results: accurate quantification, qualitative search for presence/absence of transcripts, detection of alternative splicing etc.
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