Take-home exercise announcement

This assignment (https://github.com/shirleyxueli41/Tufts_workshops/blob/main/IGDH-1001_2024Feb/Take-home%20exercise.md ) is structured into two main exercises focused on exploring and analyzing biological data related to the microbiota of diverse vinegars. Exercise 1 is divided into three parts: * 1.1 asks students to research a specific bioproject (PRJNA891065) on the NCBI database to summarize the project, count the biosamples, and identify the genes sequenced. * 1.2 involves reading and summarizing the abstract of a research paper associated with the bioproject, focusing on the characterization of vinegar microbiota using omics tools. * 1.3 requires detailed information about a specific SRA run (SRR21926282), including sequencing instruments, strategy, read type, total reads, and sample details from the biosample page.

Exercise 2 instructs students to review materials on a "Hands-on session," identify specific SRA runs from given samples, process them using Galaxy, and analyze the top 3 genera and create a Krona plot for each sample. The exercise emphasizes comparing samples from wineries and breweries. The assignment concludes with writing a report that includes answers to all questions, results from Galaxy analyses, screenshots, and a summary comparing winery and brewery samples. The rubric outlines the points allocation for each task, totaling 25 points.

Assignment - Rubric (25 points total) 1 Exercise 1.1 (1 point for each question, 3 points in total)
2 Exercise 1.2 (2 points)
3 Exercise 1.3 (1 point for each question, 5 points in total)
4 Exercise 2: * Identify the SRA ID (1 point for each sample, 4 points in total) * Process the SRA in Galaxy and identify the top three genera for each sample. (1 point for each sample, 4 points in total) * Visualize the results with Krona plots (1 point for each sample, 4 points in total) * Summarize the results, with a comparison between winery and brewery samples. Remember to compare between winery samples and brewery samples. (3 points)

Please don't hesitate to reach out if you have any question. Shirley Li: xue.li37@tufts.edu

Warning: we ask to identify the top three genera for each sample instead of species in the take-home exercise.