Can someone help clarify ways to measure coverage? Here is my current understanding, but I'm not sure about 2. 1. Library size is one way to measure coverage, and it is equal to 2. The number of reads that align to a particular gene. I hope this makes sense. Thanks!
- This is measure of sequencing depth ("library" is different; it refers to cDNAs not reads)
- No; this is just a way to filter out low-count genes; has nothing to do with sequencing depth or coverage. Also, the number of reads that align to a particular gene isn't very informative because highly-expressed genes and genes with longer transcripts will obviously have more reads aligned to them.
Also, coverage (distinct from sequencing depth) estimates how many times each base in a genome or transcriptome is sequenced, on average. It's not a useful metric for RNA-seq because when a gene is highly expressed, it's going to have more sequencing reads than a lowly-expressed gene.