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Questions and improvements #3

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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

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@Phlya
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Phlya commented May 16, 2021 •
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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
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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
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no, sorry...

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

@gfudenberg any idea what we meant by that?

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@Phlya @gfudenberg