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dbmi-pitt / aurora-meta

Aurora metadata portal
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Compute access: Justin Balko / Agi #12

Open ropelews opened 5 years ago

ropelews commented 5 years ago

Contacted user 7/1/19

Hello Justin,

This is Uma Chandran, one of the bioinformaticians from Pitt. Adrian forwarded me your email and I wanted to follow up on the analysis plan.
I have not done ERV analysis myself but, from what I understand,it sounds like you will need to remap to the genome, not the transcriptome, and you will not reject multi-mapped reads. From what I understand from the ERV publications, this is not the standard RNA Seq pipeline but a custom pipeline to detect ERVs.

As far as computing, as Adrian points out, ideally you should do the work at Pittsburgh Supercomputing Center (PSC) where the data files are stored. Under the data use agreement for this project, there may be restrictions on moving raw data files (fastq and BAM) out of PSC, i.e, the data hosting center. I am not absolutely sure about this but Adrian and others, please correct me if I am wrong.

Setting up computing at PSC for you and for members of your team is straightforward. You just need an XSEDE account and once you are given permissions to the folders, you can compute using the PSC nodes. I am also cc'ing Alex Ropelowski, PSC scientist. He and/or I can provide instructions and walk you through this process. We can also work out details of where you will store your processed and results files at PSC or you can move them off PSC, if you prefer.

Please let us know if this will work for you and if you need help getting started. If on the other hand, Adrian and others feel that it is Okay to move fastq files off PSC, we can set up a way for you to copy them.

regards, Uma Chandran

Reply from Balko, Justin justin.balko@vumc.org

Sorry all – I didn’t realize he (Agi) was out of the country. Will follow up in a week when he returns.

ropelews commented 5 years ago

Email sent 7/3/19 with instructions for obtaining an account:

Justin and Agi,

To get access to our computational facility, please do the following:

  1. Create an XSEDE portal account: To create an XSEDE Portal Account, visit the portal website at portal.xsede.org.
  2. Email the portal ID to ropelews@psc.edu and tmaiden@psc.edu so you can be added to the project grant. You will receive several automated emails from the process. The last email will direct you to the website apr.psc.edu which is used to create your initial password or reset your password (if you already have an account).
  3. Once your account is created, please email ropelews@psc.edu and tmaiden@psc.edu so we can set up a call to help you to get started. Alex.
ropelews commented 5 years ago

7/18/2019: Tom and Alex had a phone call with Agi and gave him the information that he needed to get started with using Bridges and accessing Aurora data.

7/25/19: After the Aurora call, Tom checked and it looks like Agi ran a single job. Tom will follow up with him to see if he needs additional assistance.

tmaiden2 commented 5 years ago

Agi has indicated that he has no issues. Will follow up shortly to determine progress.