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loosolab / TOBIAS_snakemake

Snakemake pipeline for running TOBIAS analysis
MIT License
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TOBIAS_snakemake: BINDetect supplementary, CreateNetwork & Additional programs output generation #7

Closed deep-buddingcoder closed 1 year ago

deep-buddingcoder commented 1 year ago

Hi Mette,

I am curious to know,

If TOBIAS_snakemake can generate

A.) BINDetect supplementary output: (https://github.com/loosolab/TOBIAS/wiki/BINDetect) 1.) to predict binding for a single condition (which will turn off any estimation of differential binding)? 2.) for a timeline of ATAC-seq experiments?

B.) CreateNetwork output (https://github.com/loosolab/TOBIAS/wiki/CreateNetwork)?

C.) output by executing additional programs (https://github.com/loosolab/TOBIAS/wiki/Additional)?

Thanks Deep

msbentsen commented 1 year ago

Hi Deep,

In regards to single conditions, yes, if you only put one condition in the configuration file, BINDetect will be run on this condition exclusively (without differential binding). E.g.:

data:
  Bcell: [data/Bcell.bam]

run_info:
   (....)

If you have a timeline, these can be added to the configuration file as well, e.g.:

data:
  day1: [data/day1*.bam]
  day2: [data/day2*.bam]
  day3: [data/day3*.bam]

Any additional tools are not added, but can be run manually after the run. The majority of the tools in "Additional" are not used for analysis specifically, but are helper functionality to work with the data in general.

deep-buddingcoder commented 1 year ago

Hi Mette, I appreciate your comments/guidance. I will work on this. Closing the question thread. Thanks Deep