4/12/19

Objectives/Goals: The objective of this lab was to practice computing data, so that we can later use the same method on our own data. The goals were to make a directory, obtain the sample data, demultiplexing the data, controlling the quality of the data, visualizing a table, and diversity analysis.

Procedure:

1. Open terminal
2. Make a directory (mkdir qiime2-moving-pictures-tutorial cd qiime2-moving-pictures-tutorial)
3. Open sample data (wget \-O “sample-metadata.tsv” \”https://data.qiime2.org/2019.1/tutorials/moving-pictures/sample_metadata.tsv”)
4. Make a new directory (mkdir emp-single-end-sequences)
5. Demultiplex the sequences (qiime demux emp-single \
   –i-seqs emp-single-end-sequences.qza \
   –m-barcodes-file sample-metadata.tsv \
   –m-barcodes-column BarcodeSequence \
   –o-per-sample-sequences demux.qza)
6. Make a file that can be visualized (qiime demux summarize \
   –i-data demux.qza \
   –o-visualization demux.qzv)
7. Open QIIME2view and drag file into viewer
8. Use DADA2 method for quality control (qiime dada2 denoise-single \
   –i-demultiplexed-seqs demux.qza \
   –p-trim-left 0 \
   –p-trunc-len 120 \
   –o-representative-sequences rep-seqs-dada2.qza \
   –o-table table-dada2.qza \
   –o-denoising-stats stats-dada2.qza)
9. Make a feature table and visualize (qiime feature-table summarize \
   –i-table table.qza \
   –o-visualization table.qzv \
   –m-sample-metadata-file sample-metadata.tsv
   qiime feature-table tabulate-seqs \
   –i-data rep-seqs.qza \
   –o-visualization rep-seqs.qzv)
10. Visualize phylogeny (qiime diversity core-metrics-phylogenetic \
    –i-phylogeny rooted-tree.qza \
    –i-table table.qza \
    –p-sampling-depth 1109 \
    –m-metadata-file sample-metadata.tsv \
    –output-dir core-metrics-results)

Conclusion/Future Goals: This lab taught me a lot about the complex processes of bioinformatics. I learned that the terminal can be used with many different commands to make directories, save files, make files compatible for visualization, and a lot more. These commands are very useful in analyzing the diversity of samples. In the future, I hope to be able to use these commands and remember the processes without having to refer to the tutorials. I think these skills will help me in my future research when analyzing bioinformatics.