4 ms·

A much bigger problem than the compression format is the fact that biologists over-sequence. You don't need 500x coverage, trust me, please learn to design your

• chrisamiller 4y ago
  That's a pretty expansive statement. Are you doing error-corrected sequencing to look for rare mosaic variants? Do you care about transcripts expressed at very low levels? Are you trying to tease apart subclonal variation in cancer? All of these could be good reasons to sequence deeply. If anything, I see the opposite problem much more frequently: People who cheap out on the sequencing depth, neutering their statistical power!
• biotinker 4y ago
  > You don't need 500x coverage, trust me, please learn to design your experiments Maybe you don't need 500x coverage, and if you don't, then I'm glad you're not sequencing to that depth. But please don't tell other people they're doing something wrong when you don't understand their use cases. Making the blanket statement that 500x coverage is generally not needed for any experiment is patently false. I've built clinical liquid biopsy tests where it was a QC failure if particular sites of interest were under 5000x coverage. Sequencing such sites to only 500x coverage would be a waste of everybody's time, because it would be impossible to gain meaningful results from so little data.
• pneumic 4y ago
  Some people do need it for R&D.