I have a bulk RNA-seq dataset that has a bias. If you plot the number of total mapped reads and of uniquely mapped reads after the mapping, you see some (many) samples have very low uniquely mapped reads compared to the other ones (in between 2-3M reads). The other samples have way more - between 15-20 million uniquely mapped reads as an average. (additional info: mapping was done with STAR. total coverage of samples after sequencing is not bad, explored with FastQC)
That first group of samples I mentioned is important for the condition, for which the alternative of just kicking out those samples from the dataset is not desired. Downsampling the others to go to 3 million uniquely mapped reads for all was discussed. I was wondering if this is ok or if it´s too low.
Q: What is the minimum number of uniquely mapped reads required in bulk RNA-seq? Thank you.