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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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Meeting w/ Dalila #945

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

Hi Tao,

Yes Thursday (tomorrow) at 5pm works. Will you send a Zoom invite?

Best Dalila

twang15 commented 2 years ago

Hi Dalila,

It should be a quick meeting for ~ 15 minutes. I am going to send you a link for half a hour.

Best, Tao

twang15 commented 2 years ago

Hi Xiao and Dalila,

I have sent you a globus endpoint to test the file sharing with you. Please let me know whether you can download the data.

Best, Tao

twang15 commented 2 years ago

Hi Tao, Alex

Just following up further, I know Tao and Xiao are in touch to finding a best way for data transfers through Globus. Xiao has now shared a globus endpoint folder on our hpc cluster that you can use to upload your data. If that works for you, then I’d suggest to upload a data set for one sample for testing purposes, before uploading the rest of the samples.

Best Dalila

twang15 commented 2 years ago

Hi Alex and Annika,

Soumya and I have met Dalila and Xiao. We figured out two options for data transfer: SCP and Globus, and we decided to try Globus first (thanks Carolin for mentioning this).

Dalila will need the list of datasets that will be shared with them. She mentioned the following needs: Long-read RNA datasets about two brain regions: Hippocampus and dACC Short-read RNA-seq datasets (for QC and other purpose she needs bulk RNA datasets, but we do not have them. So instead she wants single-cell datasets in the hope to do pseudo-bulk analysis)

Please let us know the datasets that satisfies her needs.

Thanks, Tao

twang15 commented 2 years ago

I have set up Globus with Xiao and transferred the datasets to them.