Closed AntoniaChroni closed 5 hours ago
To run and summarize Cell Ranger count for single or multiple libraries for sc-/sn-RNA-Seq Analysis in 10X Genomics data across the project.
Closes #12. Closes #17. Closes #16.
Tell potential reviewers what kind of feedback you are soliciting.
Please run:
submit-multiple-jobs.sh
Instructions on how to run the file can be found in the README file.
README
Please also confirm the following:
j1.sh
j2.sh
waiter.sh
./util/run_cellranger.py
summarize_cellranger_results.py
Here we use CellRanger v8.0.1 and run by default parameters, i.e., there are no constraints to the number of cells to be considered per library.
@sharonfreshour Everything has been updated accordingly. Just so you know – suggestions not being directly accepted have been done at once here 0c2d72aa23ca80abb9ee52afdb371b91ad297299.
Purpose/implementation Section
Type of change
What scientific question/module of analysis is your analysis addressing?
To run and summarize Cell Ranger count for single or multiple libraries for sc-/sn-RNA-Seq Analysis in 10X Genomics data across the project.
What GitHub issue does your pull request address?
Closes #12. Closes #17. Closes #16.
Directions for reviewers
Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please run:
submit-multiple-jobs.sh
Instructions on how to run the file can be found in the
README
file.Is there anything that you want to discuss further?
Please also confirm the following:
README
file contains enough clear documentation on running the module.j1.sh
file for clarity.j2.sh
file for clarity.submit-multiple-jobs.sh
file for clarity.waiter.sh
file for clarity../util/run_cellranger.py
file for clarity.summarize_cellranger_results.py
file for clarity.Results
What was your approach?
Here we use CellRanger v8.0.1 and run by default parameters, i.e., there are no constraints to the number of cells to be considered per library.
Reproducibility Checklist
Documentation Checklist
README
and it is up to date.