You have been provided with 6 sets of reads, representing two different sample conditions. Three are from bacteria incubated in seawater, simulating planktonic conditions (Plk), and three are from bacteria collected immediately after venting from squid (Vnt). All datasets are 100bp single end reads, produced from an Illumina HiSeq2500. The reads have been quality trimmed with the BBduk plugin to remove low quality bases.
To assist with assigning sample conditions in the DESeq2 analysis, the sample condition has been added as a metadata field on each sequence list. To view this, select one of the sequence lists and click the Info button above the sequence viewer. You will see a "Sample condition" metadata field that is assigned as either "planktonic" for Plk sequence lists, or "Squid-associated" for Vnt lists.
Now we will map the reads to the reference sequence. Select all 6 the read lists (hold down shift to bulk-select), and go to Align/Assemble → Map to Reference. Set the reference sequence to the provided file NC_006841 using the Choose button. Because we want to create separate assemblies for each read set, check the option to Assemble each sequence list separately. Under Results choose to Save contigs, Save in sub-folder, and Save assembly report. All the other settings can be left as the defaults.
Note: if you are working with a genome containing introns, use the Geneious RNA mapper or Tophat plugin to map your reads instead of the standard Geneious mapper
Your settings should now look as in the screenshot below. Click OK to start the mapping.
Once the mapping has finished (it may take some time), you will see 6 assembly documents in a new subfolder. To calculate and compare expression levels, go to Exercise 2.