I would like to add homer motif analysis functionality to the pipeline beyond just for differential peaks (DiffBind output). Right now, homer motif calling is used in rule HOMER in peak_utils.smk.
I would now like to have an additional homer rule or two to:
-- run directly on the macsNarrow peak output
-- run directly on the macsBroad peak output
-- this version should only run when assay is "chipseq" [no impact on the original rule]
-- analysis should not run when the number of peaks is less than 20 or greater than 45,000
I want the whole folder tarred. I also want a copy of the file called "knownResults.txt" saved outside the tarball (keep the original within the tarball). To prevent naming issues, please save the duplicate version as {name}.{PeakTool}.homer.knownResults.txt or something similar.
I would like to add homer motif analysis functionality to the pipeline beyond just for differential peaks (DiffBind output). Right now, homer motif calling is used in rule HOMER in peak_utils.smk.
I would now like to have an additional homer rule or two to:
-- run directly on the macsNarrow peak output
-- run directly on the macsBroad peak output
-- this version should only run when assay is "chipseq" [no impact on the original rule]
-- analysis should not run when the number of peaks is less than 20 or greater than 45,000
I want the whole folder tarred. I also want a copy of the file called "knownResults.txt" saved outside the tarball (keep the original within the tarball). To prevent naming issues, please save the duplicate version as {name}.{PeakTool}.homer.knownResults.txt or something similar.