Should we change our q-value filtering settings?

jfear / s2rnai

S2 Cell RNAi Project

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Should we change our q-value filtering settings? #35

Closed jfear closed 7 years ago

jfear commented 7 years ago

I think as a group we should discuss the current thresholding. Everyone needs to look at the website, and then we can look at some of the counts/plots @isabelleberger will be making to decide how we want to proceed.

To Do

[x] Look at meme/fimo website

wyjhxq commented 7 years ago

I will look the paper to see how they get the q-value. Maybe this will help a little bit.

jfear commented 7 years ago

We have decided to proceed with trying to use a ranked percentile to threshold motifs. This method has been used in:

Siahpirani, Alireza F., and Sushmita Roy. 2017. “A Prior-Based Integrative Framework for Functional Transcriptional Regulatory Network Inference.” Nucleic Acids Research 45 (4): e21.

We are also exploring using accessibility information (Histone marks, DNAse I hypersensitivity).