Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Questions and improvements #3

Open
6 of 12 tasks
Phlya opened this issue May 16, 2021 · 2 comments
Open
6 of 12 tasks

Questions and improvements #3

Phlya opened this issue May 16, 2021 · 2 comments

Comments

@Phlya
Copy link
Member

Phlya commented May 16, 2021 •
edited

Questions that came up during the Tuesday meeting with Geoff

  • how to let users specify resources like thread?.
    • tell them to change the snakefile
    • make a separate resources file that can have cluster or local config that is then read by config yaml (some manual work), # todo ?{resources[‘expected’][‘threads’]}
    • wait for snakemake to change its format
  • loops/dots naming consistency across library
  • Test what happens with empty annotations.tsv or other files.
  • Think if pileups should be split into TAD pileups and annotation pileups?
  • should providing no samples to call_tads by default calculate them across all input datasets?
  • add some comments to yaml showing sections, move resolutions up to genome zone
  • how to enable saddles against a bigwig (e.g. GC content) or other sample?
  • insulation for multiple windows in one job
  • should insulation or call_tads be split to a separate rule for strong boundaries
  • how to do plotting?
  • write something about analyses that have a reference dataset …
  • (how) would this work for a single-cell dataset?
@Phlya
Copy link
Member Author

Phlya commented Feb 10, 2023

should insulation or call_tads be split to a separate rule for strong boundaries

@gfudenberg any idea what we meant by that?

@gfudenberg
Copy link
Member

no, sorry...

should insulation or call_tads be split to a separate rule for strong boundaries

@gfudenberg any idea what we meant by that?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@Phlya @gfudenberg