My lab ordered paired end sequencing, and we received a reported coverage of 30 million reads per sample.
Just to confirm - this means that there are 30 million reads across both directions? So, 15 mil per end in the paired end, so after alignment with TopHat2/counting with htseq-count, I should expect there to be about 15 million reads (i.e., read-pairs) for each sample?
Or should I expect to see 30 million reads, representing 30 million pairs/60 million total ends?
Thank you for the sanity check!