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A LIMS for ENCODE submitting labs.
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Data submission to ENCODE: cs-393 #127

Open twang15 opened 3 years ago

twang15 commented 3 years ago

ChIP-seq experiment 393 submission to ENCODE

twang15 commented 3 years ago

Error message: WT input pB-12888 on ChipseqExperiment pCS-393 doesn't have an upstream control experiment record.

Root cause: WT library sequencing result in SREQ-323 is not ready yet.

twang15 commented 3 years ago

Hi Tao, We don’t have a previous experiment ( we only received the HEY2-N Rep3 and Rep4 samples from Chicago). I added the wild-type control.

Thanks, Joan

twang15 commented 3 years ago

Hi Joan,

Thanks a lot for your confirmation and help to fix the control. Have a nice weekend!

Best, Tao

twang15 commented 3 years ago

HI Tao,

Not sure why Chicago sent rep3 and 4. This is not what they normally do when we didn’t receive 1 and 2. Maybe they were contaminated on their side and just repeated it.

Thanks, Annika

twang15 commented 3 years ago

Annika:

https://www.encodeproject.org/experiments/ENCSR286OIN/

There are a few things that have to be fixed here:

  1. Biosample summary: not sure where the NONE comes from in the text
  2. One of the biosamples doesn't have a GM
  3. This ChIP says that it's HEY2 but it's actually JAZF1 (Cory mislabeled the tubes!!!!) --> we can delete the fastqs here and submit them as JAZF1 (the real HEY2 is being sequences at the moment)?

@twang15

twang15 commented 3 years ago
  1. This ChIP says that it's HEY2 but it's actually JAZF1 (Cory mislabeled the tubes!!!!) --> we can delete the fastqs here and submit them as JAZF1 (the real HEY2 is being sequences at the moment)?

Which ChIP is JAZF1? The fastq files on the portal cannot be deleted. At the best, we can ask DCC to change the experiment meta data.

twang15 commented 3 years ago

SREQ-323 for the wild-type control is available, wait for further notification for submission from Annika because of the ongoing contamination issue

twang15 commented 3 years ago

Hi Annika,

Previously, cs-393 (https://github.com/nathankw/pulsar_lims/issues/127 and https://www.encodeproject.org/experiments/ENCSR286OIN/) has an issue and here was your response at that time:

This ChIP says that it's HEY2 but it's actually JAZF1 (Cory mislabeled the tubes!!!!) --> we can delete the fastqs here and submit them as JAZF1 (the real HEY2 is being sequences at the moment)?

What is the current status of this issue?

Thanks, Tao

twang15 commented 3 years ago

Error message from DCC: https://www.encodeproject.org/experiments/ENCSR286OIN/

  1. Missing biosample characterizationView description of Missing biosample characterization in a new tab
  2. Missing possible_controlsView description of Missing possible_controls in a new tab
  3. Missing nih_institutional_certification
twang15 commented 3 years ago

Steps to proceed

  1. Submit a new empty experiment (new_ex) without fastq files
  2. Move fastq file of the current cs-393 to the new_ex
  3. submit new fastq files to cs-393
  4. Swap the fastq files on SCG as well

From meeting memo: 04/01/2021, https://docs.google.com/document/d/18HWBgcL8nrYF90-JcYRWcwAOJOuQenXJm-6X_4HeK3s/edit?pli=1#

FASTQ swap: let DCC know when the new experiment is posted without fastqs, so we can do the fix. https://www.encodeproject.org/experiments/ENCSR286OIN/

twang15 commented 3 years ago

Wait for Wet lab's notification to proceed.

twang15 commented 3 years ago

Hi Annika,

What is the new experiment for me to submit before DCC do the fastq swap?

Thanks, Tao

AnnikaWeimer commented 3 years ago

It's probably HEY2 (likely JAZF1 and HEY2 got mixed up by Cory). But Alec first want to check this )for this he needs access to the fastq files)

Annika K. Weimer, PhD Project Lead ENCODE - Snyder lab

Stanford Medicine – Department of Genetics Center for Genomics and Personalized Medicine

@.**@.> +1 ‭(650) 724-4044

On Apr 2, 2021, at 1:38 PM, twang15 @.**@.>> wrote:

Hi Annika,

What is the new experiment for me to submit before DCC do the fastq swap?

Thanks, Tao

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twang15 commented 3 years ago

Hi Annika,

How shall we proceed for cs-393? You can check out its history: https://github.com/StanfordBioinformatics/pulsar_lims/issues/127

Best, Tao

twang15 commented 3 years ago

  1. Annika will merge cs-380's and cs-393 replicates into one experiment.

  2. Submit this experiment cs-380 (https://pulsar-encode.herokuapp.com/chipseq_experiments/380), except fastq files.

  3. DCC will move cs-393's fastq files cs-380 (on the portal)