How to use DLM model to predict probe sequencing depth? #2
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XiangjiangWang,
Hi. Thanks for your work on DLM model. I am using DLM predict the sequencing depth of probe which design from bacterial genome. However, I have two questions that I am confused about and would like to ask you.
(1) The article mentions the use of NUPACK to calculate the probes feature, such as free energy, I calculated Pfunc, dG (kcal/mol) and MFE using Tube, tube_analysis func of NUPACK, but do not match to the fields in the json file of model you provided, which "K(obs) ", "nG<x t^>", "nG[x]{t^*}", "nG[x t^]", etc. How can I calculate these feature parameters in the json file?
(2) I have a batch of probe sequences from bacterial genome, how should I use your model for depth prediction of my probes? Which model should I use, NGS_synthetic, or HYB_DSP, and what are the steps?
I am looking forward to your reply.