Versions Compared

Old Version 20

changes.mady.by.user James I. Vanee

Saved on

compared with

New Version 21

changes.mady.by.user user-d2c4e

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  1. Project Initiation
    • Requires personal contact with lab director
    • Charlotte or Sharon sets up project in redmine
  2. Sample submission: client goes to http://sorghumdiversity.maize.cornell.edu/ to get the required steps, and upload their information to attempt to get approved to send DNA samples
  3. Client sends DNA samples to the lab
  4. Charlotte sets up project in redmine
  5. DNA samples begin moving through various lab steps; redmine updated at various steps
  6. Client sets up customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php
  7. DNA samples tested and if okay, Charlotte sets up a cost issue in redmine so Theresa knows what to bill.
  8. Customer is invoiced
  9. DNA samples begin moving through various lab steps; redmine updated at various steps
  10. SampTrac is used to update HTS database entries and create barcodes for DNA and library plates.
  11. Libraries are submitted for sequencing (sometimes more than once)
  12. Raw Data -> Data Files
    • QC scripts run
    • Pipeline can be Tassel, or Fei Li's pipeline
  13. Data Interpretation
    • "manual" / "art"
  14. Data Distribution
  15. Data storage for X period of time

...

sample submission interface fields and database schema

QC Scripts

"SampTrack" C# windows program to interface with GBS for setting up pools etc.

...

redmine project management

  • Project initiation
    •   create project in redmine
  • Individual plate tracking
    • Can note if a plate failed somewhere in the process and link it to the redone plate.
    • Can link billing information so we know if the plate has been paid for

Data Distribution

  • Currently manual
    • either "hapmap table" by email, or dropbox or physical hard drive if client wants raw data

billing

Misc operations

...

  • QC Scripts
  • Comments and request changes for QC output
  • Besides the changes I listed above, but the biggest bug is that the scripts look for the cut site overhang and then the barcode.  Barcodes containing the cut-site overhang are not recognized and we see it as 0 reads.  The data pipeline does barcode and cut-site recognition simultaneously and so you still get data for these barcodes.

Samptrack

  • build rich enough interface for web? extend and maintain c# "product"?
  • Custom DB queries desired added functionality:

...