Assignment_3_ANS

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University of British Columbia *

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475

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Biology

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Jan 9, 2024

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pdf

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MICB 475 Assignment #3 Complete the following worksheet using the mouse dataset and submit to Canvas as a PDF. TAXONOMIC ANALYSIS: After you generate the taxabarplot, download the figure under download à SVG (bar) and paste it here: Ensure the taxonomic rank to set to at least 2 or higher. Rank 1 would not resolve anything significant. Below is an example at rank 4: recip.462.WT.PD3.D49 recip.466.ASO.PD3.D7 recip.460.WT.HC3.D21 recip.467.WT.HC3.D49.a recip.463.WT.PD3.D7 recip.465.ASO.PD3.D7 recip.463.WT.PD3.D21 recip.411.ASO.HC2.D49 recip.539.ASO.PD4.D7 recip.459.WT.HC3.D14 recip.459.WT.HC3.D49 recip.465.ASO.PD3.D14 recip.456.ASO.HC3.D49 recip.411.ASO.HC2.D14 recip.539.ASO.PD4.D14 recip.413.WT.HC2.D7 recip.391.ASO.PD2.D14 recip.462.WT.PD3.D7 recip.412.ASO.HC2.D14 recip.540.ASO.HC4.D7 recip.538.WT.PD4.D21 recip.460.WT.HC3.D14 recip.462.WT.PD3.D14 recip.536.ASO.PD4.D49 recip.403.ASO.PD2.D21 recip.467.WT.HC3.D49.b recip.461.ASO.HC3.D49 recip.540.ASO.HC4.D14 recip.537.WT.PD4.D21 recip.290.ASO.OB2.D1 recip.459.WT.HC3.D21 recip.463.WT.PD3.D14 recip.401.ASO.HC2.D7 recip.391.ASO.PD2.D7 recip.391.ASO.PD2.D21 recip.460.WT.HC3.D7 recip.462.WT.PD3.D21 recip.400.ASO.HC2.D14 recip.461.ASO.HC3.D21 recip.411.ASO.HC2.D21 recip.458.ASO.HC3.D21 recip.412.ASO.HC2.D7 recip.464.WT.PD3.D14 recip.389.WT.HC2.D21 recip.220.WT.OB1.D7 recip.458.ASO.HC3.D49 recip.461.ASO.HC3.D7 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Relative Frequency Sample Name: ANS
MICB 475 DIVERSITY ANALYSIS: What did you decide on for rarefaction depth (ie. Sequencing depth cutoff)? Explain why. Explanation should include: based on the research question, refer to table.qza file using the slider to optimize sample size and maintain a good number of reads/features based on the alpha rarefaction curve where it plateaus to ensure ASV saturation. You should be a looking at the observed features in the alpha rarefaction curve. Sampling depth should be between ~500 – 4400. Anything below does not reach saturation of ASVs and anything above results in significant loss of reads (<50% features). Pick one of the ALPHA diversity metrics and use the donor_status category to fill in the sections below: EXAMPLE Which metric did you pick: Piloue’s Evenness Paste the graph output below ( in the qiime2 viewer, there is an option of downloading the figure as a SVG file): What was the q-value? Is this significant? q-value = 0.000002, yes significant Healthy (n=24) PD (n=23) 0.58 0.60 0.62 0.64 0.66 0.68 0.70 0.72 0.74 0.76 0.78 0.80 0.82 0.84 0.86 donor_status pielou_evenness
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