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title: Thesis feedback
tags: [Group Meeting]

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# Thesis feedback
###### tags: `Group Meeting`

## Comments from E1

* [x] b/w printed color figures *ignored*
* [ ] swap Charpter 2 and 3
* [x] Grammatical mistakes *too general*
* [x] "none of contiguity, completeness, or correctness can dominate PDR". What is dominate? *used "overwhleming impact", but also can explain more "in the sense of that PDR ..."*
* [x] clearly state the input and output *revised pipeline diagram*
* [x] clearly state the meaning of the kth element and the meaning of the jth row *added a line*
* [x] define progeny and basic concepts like genetic linkages *add footnote and genetic map definition*
* [x] formally define the loss. How do you compute the similarity between joints? You need to state them clearer. *add E-value stuff and better figure explanation*
* [x] For the figures, indicates what are the genomes *clear enough*
* [x] explain whythe CAST method can work for polyploidy *clear enough*
* [x] rewrite the sentence in the first 3 lines
* [x] comment on the effect of repeats for your PDR metric
    *show by different repeat solution(max, min)*

## Comments from E3
* [x] compare CAST with genetic-based methods. *all are no longer maintained, can implement one if really need.*
* [x] explain why SALSA was not used in 2.3.3
    *no Hi-C data available for this dataset*
* [x] add a dataset with known reference genome to access correctness *already has A. Thaliana*
* [x] compute PDR for result 2.3.6 (PDR by # progeny and seq depth) *added*

## Comments from E2
* [x] cite their papers *cited*
* [x] More explanations for Figures and tables. *added*
* [x] supporting evidences for polyploidy *explained in future work (original  version)*
* [x] Add explanation to Figure 2.1 *added*
* [x] Some important concepts such as heterozygotes and polyploidy should be introduced in the Chapter 1 *added by footnote*
* [x] Section 2.2.2. In text, the definition for genotype vector is given for multiple progenies. However, Figure 2 depicts a scenario in which there is only on progeny. *the definition is clear enough*
* [x] Page 3, “by abduction”? *added footnote*
    ![](https://i.imgur.com/OJNnzC8.png)