| Tuesday | Thursday | |
| 8/23 & 8/25 | N/A | N/A |
| 8/30 & 9/1 | N/A | Due: HPC sponsorship request Getting started with Unix and the HPC: ssh to UA HPC Add to PATH |
| 9/6 & 9/8 | Assigned: MG_HW1 (25 pts): Decide a “person” for your microbiome analyses. Write a description of the person for your methods section. Write a first draft of the introduction to your project. Due: Email us your github user id | Assigned: C_HW1 (30 pts) write a shell script to perform “cat -n” Getting started with Gihub: Create abe487 github repository Github ssh keys |
| 9/13 & 9/15 | Assigned: MG_HW2 (25 pts): Download 8 microbiomes for your “person” using the SRA toolkit (1 time point across 8 body sites). Create a samples table that lists metadata for each of the microbiomes including information about the person and the total number of sequences. Write a description of your methods for downloading the sequence data. | Assigned: C_HW2 (30 pts): create a makefile to implement a set of tasks. Quiz 1: on C_HW1 (20 pts) |
| 9/20 & 9/22 | Assigned: MG_HW3 (25 pts): Perform quality control on your 8 microbiomes. Update the samples results table with the number of sequences for each sample after QC. Write up your QC methods including the cutoffs used for quality control. Due: MG_HW1 and MG_HW2 Due: C_HW1 (this due date was extended) | Assigned: C_HW3 (30 pts): write a perl script with a greeting “hello world” Due: C_HW2 Quiz 2: on C_HW2 (20 pts) |
| 9/27 & 9/29 | Assigned: MG_HW4 (25 pts): Perform a metagenomic co-assembly using data from your QCed microbiomes. Write up your methods and create a summary table of the statistics for the assembly in your results section. Due: MG_HW3 | Due: C_HW3 Quiz 3: on C_HW3 (20 pts) |
| 10/4 & 10/6 | Assigned: MG_HW5 (25 pts): Recruit reads from your microbiomes back to the assembled contigs using Bowtie. Write up your methods and write up results on the total number of reads that you were able to recruit back to assembled contigs. | Assigned: C_HW4 (30 pts): write a perl script to print lines in reverse order. Due: MG_HW4 Quiz 4: on HPC (20 pts) |
| 10/11 & 10/13 | Assigned: MG_HW6 (25 pts): Perform gene finding using prodigal. Write up your methods and describe the total number of ORFs detected in your results section. Due: MG_HW5 | Assigned: C_HW5 (30 pts): write a perl script that performs the same function as the unix command “wc” Due: C_HW4 Quiz 5: on C_HW4 (20 pts) |
| 10/18 & 10/20 | Assigned: C_HW6 (30 pts): write a perl script to caclulate GC content. Due: MG_HW6 | Due: C_HW5 Quiz 6: on C_HW5 (20 pts) |
| 10/25 & 10/27 | Assigned: MG_HW7 (25 pts): Perform taxonomic annotation on your reads directly using Centrifuge. Note this protocol includes steps to download new paired end data, and remove human contamination prior to taxonomic analysis. Write up your methods and describe the output of the analysis in the results section. You will produce bar charts to include in your report. | Assigned: C_HW7 (30 pts): write a perl script to find single nucleotide variations between sequences. Due: C_HW6 Quiz 7: on C_HW6 (20 pts) |
| 11/1 & 11/3 | Assigned: MG_HW8 (25 pts): The “uber protocol” refined assembly, gene calling, and read recruitment. Due: MG_HW7 | Due: C_HW7 |
| 11/8 & 11/10 | Assigned: MG_HW9 (25 pts): Upload results to Anvio to visualize. Perform HMM profiling. Assigned: MG_HW10 (25 pts): Perform functional annotation using uproc. Write up your methods and describe the output of the analysis in the results section. Due: MG_HW8 | Assigned: C_HW8 (30 pts): find the number of shared words between two files. Due: MG_HW9 Quiz 8: on C_HW7 (20 pts) |
| 11/15 & 11/17 | Assigned: MG_HW11 (25 pts): Upload the BAM files to anvio to show read recruitment. | Assigned: C_HW9 (30 pts) Due: C_HW8, MG_HW10 Quiz 9: on C_HW8 (20 pts) |
| 11/22 & 11/24 | Assigned: Journal-club (JC) presentations Assigned: MG_HW12 (25 pts): Perform hierarchical clustering and CONCOCT genomic binning in Anvi’o. Write up your methods and describe the output of the analysis in the results section. Due: MG_HW11 | – Holiday – |
| 11/29 & 12/1 | Assigned: Final report (100 pts): Rewrite the introduction to your project based on your readings and analyses. Compile your methods and results for MG_HW1 to 12. Write up your final discussion of the results. What patterns do you see? Are these patterns consistent with the literature? What does your data look like compared to your partner? final_project_report Assigned: C_HW10 (30 pts): program for final report. Due: MG_HW12 | Quiz 10: on C_HW9 (20 pts) Due: Journal-club presentations |
| 12/6 | Due (12/6): C_HW9 Due (12/9): Final project report ; Journal-club presentations and report; C_HW10; all are due on 12/9. | -Dead Day- |
Assignments_Fall2016