DECODE The Script of LIFE

 Genomics_command_line_quiz1 For all projects, you may use your own Unix-based system and, where applicable, ensure that you are running the version of the software specified in the assignments. Alternatively, you may use the VMBox virtual machine environment provided with the course materials. Instructions on how to download and use the environment can be found on the course web site. For the following questions, refer to the class workflow and use the data in the Online materials (‘gencommand_proj1_data.tar.gz’) to answer the questions. Assume you sequenced and assembled the genome of Malus domestica (apple), and performed gene annotation. You then collected samples and ran RNA-seq experiments to determine sets of genes that are expressed in the various tissues. This information was stored, respectively, in the following files: “apple.genome”, “apple.genes”, “apple.condition{A,B,C}”. NOTE: The apple genome and the apple gene annotations for this project were extracted from the Rosace

1. Question 1 A student wants to write into a file called myfile, without deleting its existing content. Which one of the following functions should he or she use? f = open('myfile', '+') f = open('myfile', 'rw') f = open('myfile', 'a') f = open('myfile', 'r') 2. Question 2 Which of the following statements are true? A) When you open a file for reading, if the file does not exist, an error occurs. B) When you open a file for writing, if the file does not exist, a new file is created.  C) When you open a file for reading, if the file does not exist, the program will open an empty file. D) When you open a file for writing, if the file exists, the existing file is overwritten with the new file. E) When you open a file for writing, if the file does not exist, an error occurs. B, C, and D only A and B only A, B, and D only All of them are correct Question 3 Examine the following three functions that take as argument a file name

Bioinformatics Bioinformatics is a fascinating field that bridges biology, computer science, and mathematics . History :                 The term “bioinformatics” was coined in 1970 by Paulien Hogeweg and Ben Hesper. Initially, it focused on information processes in biotic systems, running parallel to biochemistry. Explosive growth occurred in the mid-1990s, driven by the Human Genome Project and advances in DNA sequencing technology .                           Let’s delve into it:                                                                         Definition: "Bioinformatics is an interdisciplinary science that develops methods and software tools for understanding biological data, especially when dealing with large and complex datasets. It involves analyzing and interpreting biological information using techniques from biology, chemistry, physics, computer science, and statistics"   Applications: Genomics: Bioinformatics aids in sequencing and annotating genomes, identi

Coursera Statistics Genomics Module #3 Statistical genomics 1. Load the example SNP data with the following code: library (snpStats) library (broom) data(for.exercise) use <- seq( 1 , ncol(snps.10), 10 ) sub.10 <- snps.10[,use] snpdata = sub.10@.Data status = subject.support$cc Fit a linear model and a logistic regression model to the data for the 3rd SNP. What are the coefficients for the SNP variable? How are they interpreted? (Hint: Don’t forget to recode the 0 values to NA for the SNP data) # recode 0 values to NA snp3 = as.numeric(snpdata[, 3 ]) snp3[snp3== 0 ] = NA # fit a linear model lm3 = lm(status ~ snp3) tidy(lm3) ## # A tibble: 2 x 5 ## term estimate std.error statistic p.value ## <chr> <dbl> <dbl> <dbl> <dbl> ## 1 (Intercept) 0.544 0.0549 9.91 3.75e-22 ## 2 snp3 -0.0394 0.0468 -0.842 4.00e- 1 # fit a logistic regression model glm3 = glm(status ~ snp3,family= "binomial&quo