Entering edit mode
3.4 years ago
whb
▴
60
Just wondering what tools should be used for sequencing saturation analysis for DNA sequencing? Most tools I found are for RNA-seq. Can these tools be used for DNA-seq as well? e.g. subSeq?
Thank you!
http://smithlabresearch.org/software/preseq/
Thank you for the reply. So do I downsample it to 10%, 20% 50% 80% of the total reads. Then align and variant call again?
Your question was about tools for saturation analysis, the tool I linked will tell you whether sequencing deeper will give you more unique coverage. I have no idea what you are working on, for this you should details to the original question. I assume variant calling.
Apology for not being clear. That exactly what I want to do: to find out if sequencing more will yield more SNPs. Is it correct to use the c_curve function in preseq to do that? Thank you again