search

StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
3 stars 1 forks source link

ENCODE data submission: replicate swap for ENCSR319GRO and ENCSR967DSJ #915

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

Hi Annika and Tao,

While reviewing the RNA-seq datasets for release, we noticed that 2 of the datasets are marked as "anisogenic" replication: https://www.encodeproject.org/search/?type=Experiment&references.@id=%2Fpublications%2Fde19555b-a49f-471c-bfbc-be3b628fe9bf%2F&replication_type=anisogenic

It seems like both datasets each have 1 replicate that is "male adult (55 years)" and 1 replicate that is "female adult", so the pairs may have gotten swapped.

Could you double check on your end and let us know if this should be corrected?

Thank you! Jennifer

twang15 commented 2 years ago

Hi Tao,

https://docs.google.com/spreadsheets/d/1SADAgiw5r9z2UVN7oybGhLwZD9ma77rrZRtqCtnEtcI/edit#gid=2133268131

Could you please double check this submission? There are mistakes. The biosamples/libaries/experiments that belong together are color coded. I can definitely see issues with these four experiments: ENCSR319GRO ENCSR350OKU ENCSR215KUO ENCSR575MQY Maybe more. Could you please check this asap?

THanks, Annika

twang15 commented 2 years ago

Hi Jennifer and Annika,

Thanks for pointing out the errors in the submission. The errors should be corrected since replicates were swapped.

Jennifer, would it be easier for you to move replicates around or shall I resubmit them?

Thanks, Tao

twang15 commented 2 years ago

Hi Tao and Annika,

Thanks for double checking the datasets!

In this case it should be easier for us to move the replicates. Please let us know which replicates need to be moved, and where they should be moved to. Also, let us know if any of the files or replicates' aliases should be updated following the move.

Thanks, Jennifer

twang15 commented 2 years ago

Hi Jennifer,

Please check out the attached correction sheet. Sorry for this submission errors.

Please let me know if you see more.

Thanks, Tao

twang15 commented 2 years ago

Hi Annika,

Sorry about the submission errors on ALS datasets.

I’ve figured out the solution with Jennifer for the entire submission. The mistake rooted in the order of the original color-coded datasets, because it is difficult for eyes to catch the subtle out-of-order entries.

Best, Tao