Merge pull request #2 from d2389758/patch-3

Update README.md

part3_consensusgenome/README.md

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 ## Part 3 Comparison between consensus and genome graphs
 
-In addition of inclusion genetic diversity in the graphs, ones could also mitigate mapping bias by adjusting reference genome to the targeted population, or so called as consensus genome approach. In this part, we replaced bases in the ARS-UCD 1.2 bovine reference genome with the most frequent allele in the the population. We consider two types of consensus:
+In addition to including genetic diversity in the graphs, one could also mitigate mapping bias by adjusting reference genome to the targeted population, or so called as consensus genome approach. In this part, we replaced bases in the ARS-UCD 1.2 bovine reference genome with the most frequent allele in the the population. We consider two types of consensus:
 
 #### 1. Major-BSW
 
@@ -10,8 +10,6 @@ We modified reference bases with major allele where frequency calculated based o
 
 We modified reference bases with major allele where frequency calculated based combined 288 animals in four cattle populations (BSW, OBV, HOL, and FV).
 
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 ![Consensus genome experiment](fig/methodpart3.png)	
 
 
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 #### 1. Creating consensus genome based on major allele
 
-We calculated two consensus, `major-BSW`  and `major-pan` where AF calculated based on Brown Swiss and combined population respectively. We provided the variants in `../data/part3/vcf_consensus` (with frequency file and the vcf files). 
+We calculated two consensus, `major-BSW`  and `major-pan` where allele frequencies were calculated based on Brown Swiss and combined population, respectively. We provided the variants in `../data/part3/vcf_consensus` (with the frequency file and the vcf files). 
 
-We modified the original reference with major variants defined in the vcf file with `vcf2diploid` tools. *Vcf2diploid* is a tool to generate parental and maternal haplotypes by replacing reference with variants from phased vcf. For our purpose, we inputted a single sample vcf with all genotypes were homozygous alternate (thus all alleles will be replaced with corresponding variants and outputted the same two fasta haplotypes). Since replacing reference allele with insertion and deletions causing genomics coordinate shift, we applied the accompanying *chain file* produced by *vcf2diploid* to convert the coordinates of the simulated reads from the original to the modified reference using local UCSC liftOver tools. 
+We modified the original reference with major variants defined in the vcf file with `vcf2diploid` tools. *Vcf2diploid* is a tool to generate parental and maternal haplotypes by replacing reference with variants from phased vcf. For our purpose, we inputted a single sample vcf with all homozygous alternate genotypes (thus all alleles will be replaced with corresponding variants and outputted the same two fasta haplotypes). Since replacing reference allele with insertion and deletions would cause genomics coordinate shift, we applied the accompanying *chain file* produced by *vcf2diploid* to convert the coordinates of the simulated reads from the original to the modified reference using local UCSC liftOver tools. 
 
 
 
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 The scripts will generate modified consensus genomes as `25_anims_major-BSW.fa` and `25_anims_major-pan.fa`. Additionally, mapping statistics generated in `compare.gz` files that are required for subsequent data analyses. 
 
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 #### 3. Data Analysis
 
 The analysis presented in the paper can be followed interactively through Jupyter notebook in [`analysis/part3_consensusgenome.ipynb`](analysis/part3_consensusgenome.ipynb) or via `binder` [![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/danangcrysnanto/bovine-graphs-mapping/master?filepath=part3_consensusgenome/analysis/part3_consensusgenome.ipynb).
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