Questions and improvements

[Phlya]

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]

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

@gfudenberg any idea what we meant by that?

[gfudenberg]

no, sorry...

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

@gfudenberg any idea what we meant by that?