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title: Group Meeting 2019/09
tags: [Group Meeting]

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# Group Meeting 2019/09

###### tags: `Group Meeting`
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# 2019/01/15
![](https://i.imgur.com/ulo2zPo.png)

half-life: 15min~2h
Collect 30 samples' turnaround time from inex:
* Blood->Plasma
* Plasma->DNA

### Pearson
![](https://i.imgur.com/oZU4rpO.png)

Pearson(FF vs. Blood->Plasma): -0.07
Pearson(FF vs. Plasma->DNA): -0.19

![](https://i.imgur.com/uHVDrzC.png)

[notebook](http://xcnc45.comp.nus.edu.sg:8888/notebooks/INEX_564_predict.ipynb)

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# 2019/12/13
**CAST**
#### Problem
2 sites far to each other, easy to get P>0.0001
#### Solution 
1. convert `distance` to `recombination rate`
2. remove progeny with largest difference sum
3. do permutation test

**NIPT**
![](https://i.imgur.com/hqtuf7U.png)
$(x,y) = \frac{\Sigma_{x \le i \le y}\ offset[i]}{total\ read}$

![](https://i.imgur.com/e4GW2Go.png)
$(x,y) = \frac{\Sigma_{x \le i \le y}\ offset[i]}{\Sigma_{x-10 \le i \le y}\ offset[i]}$



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### 2019/11/01
$\forall S \subset \mathbb{G}$
$~~~$ Let $\alpha=P(\text{read in } S|\text{fetal read})$
$~~~$ Let $\beta=P(\text{read in } S|\text{maternal read})$

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For any sample: 
$~~~~ \frac{\text{read count in } S}{\text{total read}}=f\alpha+(1-f)\beta ~~~~~~\Rightarrow~~~~~ f=\frac{r-\beta}{\alpha-\beta}$

> $\alpha$ and $\beta$ can be trained by linear fitting.

> chrY-based method is a special case where $S=chrY$

> **OBJECT: maximize $|\alpha-\beta|$ by good $S$**

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nucleosome profile => read count around nucleosome centre
![](https://i.imgur.com/A9gqCsA.png)
Pearson=0.73

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#### Better nucleosome track
FFT (window size=600)
![](https://i.imgur.com/1OQOrJq.png)

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![](https://i.imgur.com/y1ZDa7a.png)

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### 2019/09/20
Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin, ***Genome Research***, Dennis Lo.

Theory
![](https://i.imgur.com/eYLZBa0.png)
Nucleosome position
![](https://i.imgur.com/vtrtYsi.png)
Open Chromatin Region
![](https://i.imgur.com/CUKjEkH.png)



### 2019/09/13
Sanefalcon vs Y-chrom
![](https://i.imgur.com/T2sqPT3.png)
![](https://i.imgur.com/EHVWhiy.png)
Sanefalcon profile
![](https://i.imgur.com/HAVV71G.png)
nucleosome size vs. first/second peak
![](https://i.imgur.com/siTbEKQ.png)
