Contigs.Rmd

---
title: "Contigs determination and analysis:  Xenopus laevis"
author: "Bharath Manicka Vasagam, The Barski Laboratory, CCHMC"
date: "March 14, 2016"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Objective
  The objective was to determine the contigs elmination point with the Xenopus laevis genome data.

##Packages used

1. data.table
2. zoom - for interactive visualisation of plot

#Methodology
  1. Raw Data file of base pairs of **Xenopus laevis** was cleaned and tabulated as Scaffold names and Number of base pairs identified from the file **fasta.R**
  2. Then the output's cumulative distribution function was plotted. Sample quantiles of base-pairs, to determine the lowest base pair cut in the file **distribution.R**
  
# zoomed in plots:
![Output_1](C:\Users\MANN6A\Desktop\First\output1.png)
![Output_2](C:\Users\MANN6A\Desktop\First\output2.png)



From the plots it was determined that we remove contigs below 5000, 10000 base pairs this calculation was done in the file **ques.R**


#Result
  If base pairs below 10,000 was removed, we would loose 862 genes or 3.56% of total genes
  If base pairs below 5,000 was removed, we would loose 835 genes or 3.47% of total genes
  If base paird below 1,000 was removed, we would loose 580 genes or 3.01% of total genes