Long-Read 16S Sequencing (PacBio)
Long-read sequencing has certain advantages over our in-lab 16S sequencing with Illumina, like its high accuracy and species-level resolution, and the lab plans to switch to long-read sequencing in the future with the help of the Duke Microbiome Core. However, one of the drawbacks is that the pipeline takes forever; the one cohort I've run through so far took about five days to complete and often got preempted due to the sheer resources required by the run, so plan out enough time for the run accordingly and be patient with it.
To get the data from the sequencing core, create a Globus account by following the instructions here. Next, ask your contact at the sequencing core (for us, it was Graham Alexander) to add you to the data folder. To upload this folder to Isilon, click the link in the share email, which should open up the Globus Web App with the Collection and Path fields filled in, click 'Transfer or Sync to...' in the panel on the right, and fill the Collection and Path fields on the right. Click Start on the left, and you should get a green "Transfer request submitted successfully" notification. You can then check the status of the transfer on the Activity page, which can be accessed from the menu on the left.
Tip
You may need to configure a folder connection with Isilon in order to see it as an allowed collection to transfer to. To do so, follow the instructions here.
Long-read sequencing has certain advantages over short-read 16S sequencing with Illumina, like its high accuracy and species-level resolution. However, one of the drawbacks is that the pipeline takes forever; the one cohort I've run through so far took about five days to complete and often got preempted due to the sheer resources required by the run, so plan out enough time for the run accordingly and be patient with it.
To get the data from your sequencing core, create a Globus account and ask your contact at the core to share the data folder with you. To transfer the folder to your shared storage, click the link in the share email (this should open the Globus Web App with the Collection and Path fields filled in), click 'Transfer or Sync to...' in the panel on the right, and fill the Collection and Path fields on the right with your destination. Click Start on the left, and you should get a green "Transfer request submitted successfully" notification. You can check the status of the transfer on the Activity page, accessible from the menu on the left.
Tip
You may need to configure a folder connection with your shared storage in order to see it as an allowed collection to transfer to. Follow the instructions here.