PEC: starting point

[twang15]

2 emails from Juliane
proposal
dccvalidator: https://cloud.r-project.org/web/packages/dccvalidator/vignettes/using-the-dccvalidator-pec.html
synapse: https://www.synapse.org/#!Profile:3432336/profile

• need to create an account
  data submission spreadsheet : https://docs.google.com/spreadsheets/d/1c99pXa65QRmoNToQKxhgLEJtdJLSyCMf/edit#gid=429762948

[twang15]

1. Annika will look at Individual, Biospecimen
2. Tao Will look at scAtac and scNeucleus, manifest (not Longread RNA at this moment)

All the templates:
https://drive.google.com/drive/u/1/folders/1CTpJaWmMY89Isu570r_04wV8ihVMIJKu
https://www.synapse.org/#!Synapse:syn20729790 (Try the permission tomorrow afternoon)

Mike's lab internal master sheet:
https://docs.google.com/spreadsheets/d/1c99pXa65QRmoNToQKxhgLEJtdJLSyCMf/edit#gid=429762948

[twang15]

Hi Tao,

I filled out the ‘individual table’ for the psychENCODE submissions. There are quite some columns empty but I guess that’s okay. When you have access to the validator, can you run this through and see which error messages we get?

Thanks, Annika

https://docs.google.com/spreadsheets/d/1A5SP_8o0eDn60eONs4kXJ85yzVgCI0y-/edit#gid=762837246

[twang15]

Hi Juliane,

Could you help grant me access to project psychENCODE on synapse?
I have not got the right access yet.

Thanks a lot!

Best,
Tao

[twang15]

Hi Juliane,

We can provide 5 different numbers for the Q30 metadata for each scATAC-seq sample:

1. Q30 bases in read 1
2. Q30 bases in read 2
3. Q30 bases in barcode
4. Q30 bases in sample index
5. Q30 bases in read 1, read 2, barcode, and sample index, all together

We have all of these 5 numbers for each sample, so perhaps we can decide whether all of these or only a subset of these should be part of the scATAC-seq template. Annika can also comment on this when she’s back.

Best,
Soumya

[twang15]

Waiting for Annika's comment.

[twang15]

Hi Annika,

On my note, we planned to submit scRNA as first batch.
But I see that only part of the libraries have status “done”.
This submission will be partial, right?

Best,
Tao

[twang15]

Annika,,

Wonderful! We're in the process of getting the updates to the ATACSeq template approved and ready for you to use. It should be ready by next week.

Juliane.

[twang15]

Hi Annika,

could you help fill the manifest file:
https://docs.google.com/spreadsheets/d/1qH28B-j2enYrguRUJVm3vImAyzxU-f41/edit#gid=1279239600

I think that we have finished preparation of the other 3 files.
Please let me know if you any problems.

Best,
Tao