[x] Promoter region identification & quantification: With gRanges function for given distances up and downstream (parameter config -> maybe TSS_slop configs can be reused?) → like done in macroStim project for integrative analysis
[x] Consensus region to gene mapping - With Homer annotations map regions within the smallest given distances (up & downstream) to the TSS to genes → like done in macroStim project for DEA results correlation comparison
output:
counts/homerTSS_counts.csv?
counts/promoter_counts.csv
Promoter quant
Yes do. Leverage existing quantification scripts and commands (agg).
Re use tss config info
Add to doc
2 different flavors (code exists)
[x] Promoter region identification & quantification: With gRanges function for given distances up and downstream (parameter config -> maybe TSS_slop configs can be reused?) → like done in macroStim project for integrative analysis
[x] Consensus region to gene mapping - With Homer annotations map regions within the smallest given distances (up & downstream) to the TSS to genes → like done in macroStim project for DEA results correlation comparison
output:
Promoter quant Yes do. Leverage existing quantification scripts and commands (agg). Re use tss config info Add to doc