Assemble mystery data in small groups

Make a new directory for the mystery assembly

To keep things organized you should first create a new directory in your home directory for the mystery data assembly.

cd ~
mkdir mystery
cd mystery

Download the mystery data on your compute node (inside jupyter lab)

• wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1PfDOsBcHr9yQsrethTUTI1_UwJUr5lC-' -O mystery.tgz
• Unpack the mystery_data.tgz like this: tar -xvzf mystery_data.tgz. This will create a new folder called mystery_data.
• Run ls mystery_data and you’ll see this is a directory of single-end fastq files for 6 samples.

Create a new params file and modify at least one parameter

Use ipyrad2-classic to create a new params file. Since this data is already demultiplexed to sample you will need to set the sorted_fastq_path, and you will also be able to skip Step 1.

sorted_fastq_path = "/path/to/sorted_fastqs/*.gz" <- You need to change this!

Run the full assembly through step 5 and interpret the results

• And have fun ;)

Assemble the Seadragon data (optional)

If you finish the mystery data you might try running an assembly of the Seadragon data we used for the fastqc exercise, which you will recall lives in ~/test-data/SeadragonData, so you can:

cd ~/test-data/SeadragonData

And the rest of that assembly will be up to you!