Good morning metagenomics team,
I wanted to thank you for your patience, as the Nanopore delayed us. The good news is that Scott Heck from CALS IT has installed a new graphics card on the machine, and we have data Billy shared from a smaller run we did. I wanted to take a moment and review what is happening this week.
Nanopore and Lab Entry 3
For your lab entries, identify the top 5 taxa ranked by genus as the results. For the discussion, look at 2-3 in more detail and discuss their significance for the compost/e-waste recycling experiment/ State whether the results were expected or not. This is the link to the Nanopore results (opens in new window). Lab Entry 3 is due on Tuesday.
TopHat Questions
TopHat questions for Module 3 and 4 are now due on November 9th to give everyone more time to reflect and think about these topics. My goal is to prompt you to review the readings and topics for each module. Share your thoughts and let us know if you have any issues accessing TopHat.
Nephele and Quality Trimming/Read Hygiene
Several of you have noted that the marten data from the Zymo 16S (16S amplicon data) has variable quality and adapters. I have contacted both the Genomic Sciences Laboratory on campus and Zymo to ask about what adapters are used. You should always check for quality and adapter contamination. This is part of read hygiene that is critical. Note that the QIIME2/DADA2 pipelines in Nephele do offer some trimming options, though you may start with QC and submit the trimmed files for QIIME2/DADA2 16S analyses. The key is to first analyze the quality of your sequences and remove adapters, then use ‘good’ sequences for analyses.
Practice using Nephele with the Nephele activity posted on Moodle. Then, work on using Nephele to analyze the data posted on LabArchives for the marten project. This will help you answer the discussion questions (due next Tuesday) and analyze the marten dataset! These analyses could be part of your final data analysis project.
Annotations
We have reviewed the annotations for article 2 and noted that several did not complete ten annotations. I updated the grade book. Do let me know if I made a mistake. Return to the article now that you completed the KBase activities and reflected to post more comments.
HPC and QIIME/DADA2
Next week we will use the campus high-performance computer cluster Henry2 to complete the QIIME Moving Pictures Tutorial (MPT). HPC is a command-line environment and Mac users can use Terminal and Windows users will need to download MobaXTerm (free) or another terminal app. As part of next week’s unit, we posted three useful videos to get started on the HPC. We will also open the lab and work through the activity together if you are able to join us.
Forums
Post questions! I want you all to learn about metagenomics and find a tool that you can use moving forward. Bioinformatics can be frustrating. Let’s troubleshoot together.
Good news: our fungal ITS libraries will be sequenced by the GSL this weekend!
Take care! I do appreciate your questions and patience. I am so sorry we moved deadlines and caused some confusion. My intent is to give you all time to work and learn together.
CG
Laptop
The Noun Project