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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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Data Submission to ENCODE: SREQ-309 #91

Open twang15 opened 3 years ago

twang15 commented 3 years ago

Depends on proper barcode information in fastq file names. https://github.com/nathankw/pulsar_lims/issues/90

twang15 commented 3 years ago

HI Annika,

SREQ-309 and SREQ-310 have been sequenced and the fastq files and data are in the ENCODE project folder. The analyzed data is in the scRNA-Seq folder.

210205_A00509_0196_BHYKHKDRXX-Snyder-ENCODE-SREQ-309 – scATAC-Seq 210205_A00509_0197_AHWNY3DRXX-Snyder-ENCODE-SREQ-310 – scRNA-Seq

Best, John

twang15 commented 3 years ago

Hi John,

I should have checked there first. Sorry. I found the files.

Thank you so much! Annika

twang15 commented 3 years ago

HI Annika,

Sorry, didn’t you know they were there? It looked like someone was doing something with the fastq files before the count data was uploaded. Maybe Tao?

Best, John

twang15 commented 3 years ago

Hi Tao,

Did you already do something for the submission with SREQ 309 and 310?

Thanks, Annika

twang15 commented 3 years ago

Hi Annika,

I have not accessed SREQ-309 and SREQ-310. Is there anything wrong?

I think there are only several people having access to this datasets. It may be possible to find out who did what.

But I am not 100% sure whether the file systems are configured properly.

Best, Tao

twang15 commented 3 years ago

Not wrong. John was surprised that I asked him when the data will be submitted because he saw that someone did something (don’t know what) with the fastq files and he thought it was me. I was wondering if you maybe moved them to another location or started the submission already. We should try to use those data sets for the new mutiome submission from pulsar (instead of spreadsheet. Agreed?)

twang15 commented 3 years ago

Yes, we should avoid manual submission from spreadsheet as much as possible. Both of us know how error-prone the manual process is.

There are still two things preventing us from doing that Fastq file names do not have barcode. You can check another email I sent this morning about this. We have to work this out with John. Fill meta data in Pulsar. We will need tell our lab people that the system is ready for this purpose. I think you already email Minyi, so we should be a little patient on this.

Looking forward to more automatic submissions!

twang15 commented 3 years ago

Hi John,

Thanks a lot for delivering datasets to us.

I want to ask you a favor: Could you also cc me when you have a new delivery so that I know there is something new for submission?

Best, Tao