Genome 540 Homework Assignment 9

Due Sun March 15

  1. Write a program (based on the 'D-segment' pseudocode provided in lecture) to identify regions of elevated copy-number as 'D-segments', using the number of read-starts observed at every base.
  2. Allow user settable parameter values
  3. Use these values to set the transition probabilities: a11, a12, a21, a22.
  4. Observed symbols are counts of # read-starts at each position (r = 0,1,2, >=3). The emission probabilities (e1(r), e2(r)) for each symbol r in states 1 and 2 will be given by Poisson distribution with mean=m1 for state1 and mean=m2 for state 2. The means will be set based on the read coverage of input region. Note that counts 3 or greater are all lumped together in one category (represented by symbol ">=3") and its associated probability value should be calculated accordingly.
  5. The scoring scheme should be as described during lecture:
  6. Your program should output:
  7. Run the program on this file, using parameter values
  8. The input file has three columns: chromosome, position, and # of read-starts. The file was created based on the start positions of all reads mapping to chromosome 17 for individual NA12878, sequenced as a part of the 1000 genomes project. Sequencing was performed on the Illumina platform, and the reads were mapped to the human reference hg19 using BWA. The alignments are available on the 1000 genomes project website in BAM format.
  9. You must turn in your results and your computer program, using this template file. Please put everything into ONE plain text file - do not send an archive of files or a tar file, or a word processing document file. Compress it (using either Unix compress, or gzip -- if you don't have access to either of these programs let us know), and send it as an attachment to both Phil (phg (at) u.washington.edu) and Max (maxwl (at) cs.washington.edu). Name your file "[your first initial][your last name]_hw9.txt.[compression extension (i.e. .gz)]".