Download LAB 1: Finding genetic mutations in the BRCA1 and BRCA2

LAB 1: Finding genetic mutations in the BRCA1 and BRCA2 genes. Instructions: Install the BRCA diagnostic software found here: http://ccb.jhu.edu/software/BRCA-­‐diagnostic/index.shtml as well as the Bowtie software that it requires. You will run this software on a data set described below. The software will produce a report showing any mutations in either of these genes that match a known set of harmful mutations. For this lab, you will also run the additional script to compute the base-­‐by-­‐base coverage of these genes, and plot this coverage. Data download: to limit the amount of data, you can run this on an exome rather than a whole genome. Choose one of the public data sets from the 1000 Genomes project, which can be found here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/. For example, under sample HG00231, HG00232, HG00233, HG00234, HG00235 (and others) you can go to the exome_alignment directory, where you will find 4 BAM files. Two of them are subsets of the data (chr 11 and chr 20 only), and the remaining two are the “mapped” and “unmapped” reads. You only need to download the “mapped” reads. You will have to convert BAM to FASTQ in order to run Bowtie. What to turn in: (1) The mutation report. (2) A summary in your own words of what was found, describing any mutations that turned up and what they mean. Also include the size of the data set (number of reads and read length) and state how long it took the analysis to run. You should also comment on the coverage plots: how deep is the exome coverage for each gene? Your summary should be brief, less than one page. (3) Two graphs showing the coverage of BRCA1 and BRCA2 from the reads you aligned.