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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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ENCODE data submission: cs-58 ENCSR057DTZ #889

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

https://pulsar-encode.herokuapp.com/chipseq_experiments/58 https://www.encodeproject.org/experiments/ENCSR057DTZ/

twang15 commented 2 years ago

This data was partially submitted by Nathan before. It has several issues:

  1. Experiments are missing wt input control. Will be provided soon.
  2. Missing genetic modification characterization
  3. IP was only there for one of the biosamples.
twang15 commented 2 years ago

IP submitted for the other biosample as well.

twang15 commented 2 years ago

Hi Annika,

cs-58 is missing its PCR and WT control in pulsar. Do we have them anywhere else?

Best, Tao

twang15 commented 2 years ago

This is WT control:

https://pulsar-encode.herokuapp.com/libraries/10762

I am looking for the PCR.

twang15 commented 2 years ago

We don’t have a PCR of this one because it was before they decided to do validation PCRs. I will contact the DCC about that.

twang15 commented 2 years ago

Hi Annika,

The biosample for the library that you showed me has only one pooled_biosample, which failed the data validation on the portal.

Is there sth wrong here?

Best, Tao

twang15 commented 2 years ago

2022-01-17 10:38:40,560:eu_debug: <<<<<< POST biosample record michael-snyder:pB-12110 To DCC with URL https://www.encodeproject.org/biosample and this payload:

{ "aliases": [ "michael-snyder:pB-12110", "michael-snyder:pB-GM12878 batch 1 input" ], "award": "/awards/UM1HG009442/", "biosample_ontology": "/biosample-types/cell_line_EFO_0002784/", "documents": [], "donor": "ENCDO000AAK", "lab": "michael-snyder", "nih_institutional_certification": "NIC00007", "organism": "mouse", "pooled_from": [ "ENCBS547AVR" ], "source": "eadabaf1-d5b6-4b48-8847-e86461f12101", "treatments": [] }

2022-01-17 10:38:40,747:eu_debug: Failed to POST michael-snyder:pB-12110 2022-01-17 10:38:40,749:eu_debug: <<<<<< DCC POST RESPONSE: 2022-01-17 10:38:40,751:eu_debug: { "@type": [ "ValidationFailure", "Error" ], "code": 422, "description": "Failed validation", "errors": [ { "description": "['ENCBS547AVR'] is too short", "location": "body", "name": [ "pooled_from" ] } ], "status": "error", "title": "Unprocessable Entity" }

twang15 commented 2 years ago

Hi Annika,

I understand the biosample is WT and should not be pooled from any other biosamples. But, if you check https://pulsar-encode.herokuapp.com/biosamples/12110, you can see that it says:

Pooled from biosamples GM12878 batch 1 B-3036

This is why the portal complains, because it should not be pooled, right? How shall we fix this?

Best, Tao

twang15 commented 2 years ago

WT control has been submitted. Annika will ask for exception of PCR.