CBW-IMPACTT Microbiome Analysis Module 6 Lab Answers

## Question 1: How many low quality sequences have been removed? 5565 low quality reads were removed. ## Question 2: How has the per read sequence quality curve changed? From the Trimmomatic step, the tail of quality curve has been compressed to left, indicating that many lower quality reads were removed. ## Question 3: Can you find how many unique reads there are? Stated in the CD-HIT output, there are 85377 unique reads in this file. As mentioned in the tutorial, in your own data, you might find a much lower number of unique reads. ## Question 4: Can you find how many reads BWA mapped to the vector database? 234 reads mapped to the vector database. ## Question 5: How many reads did BWA and BLAT align to the mouse host sequence database? BWA found 1066 host reads and BLAT found 6 host reads. ## Question 6: How many rRNA sequences were identified? How many reads are now remaining? 2249 reads were identified as rRNA and 81822 reads remain. ## Question 7: How many putative mRNA sequences were identified? How many unique mRNA sequences? 81822 putative mRNA reads and 82741 unique mRNA reads. ## Question 8: How many total contaminant, host, and rRNA reads were filtered out? 17259 reads were filtered out. ## Question 9: How many different genera did kaiju find within our sample? 1128 genera were found. ## Question 10: What is the most abundant family in our dataset? What is the most abundant phylum? The most abundant family is Oscillibacter, and Firmicutes is the most abundant phylum. ## Question 11: How many assemblies did SPAdes produce? SPAdes produced 1084 assemblies. ## Question 12: How many reads were not used in contig assembly? How many reads were used in contig assembly? How many contigs did we generate? 59658 reads were not used, 23083 reads were used, and 1084 contigs were generated. ## Question 13: How many reads were mapped in each step? How many genes were the reads mapped to? How many proteins were the genes mapped to? Since this section was not run, the answer is given to you in case you wanted to try these later. ## Question 14: How many unique enzyme functions were identified in our dataset? 1016 unique enzyme functions were identified. ## Question 15: Using excel, have a look at the `mouse1_RPKM.txt` file. What are the most highly expressed genes? Which phylum appears most active? The two highest expressing features are flagellin proteins. Firmicutes looks to be the most active phylum. ## Visualization Questions In the format of ec00010/ ec00500. These questions are more open-ended, but some example answers are included. glyceraldehyde-3-phosphate dehydrogenase/ glucose-1-phosphate adenylyltransferase Oscillospiraceae / Oscillospiraceae Ex. The cluster of ec00010:58, ec00010:59, and ec00010:145 have higher Clostridia expression. --- All three enzymes are involved with fructose phosphorylation. The homologs across these different bacteria may not all function in the exact same way.