Hello
I just want to to what make shhh.flows denoising slowlym
Is it the ram ?
Why is it slow? Well… It’s hard? There’s a lot of data? Sorry, but I’m not really sure how to answer that one. Although you need access to RAM to be fast, I don’t think the RAM itself isn’t necessarily limiting as much as the CPU speed.
We generally find that the crappier the data and the more unique data the slower it goes.
Pat
Ok thanks for the answer
What do you mean by crappier data (in the flow file i mean)
If the data are bad it will take a long time to denoise. This can be due to a bad sequencing run, but more typically it’s because people are using bad regions of the reads. This is why with the Titanium data we advocate trimming everything at 450 flows. The data gets crappier after 450 and causes all sorts of bad things to happen including diminished denoising.