Calculate fraction of reads in promoters & enhancer regions

CCBR / CHAMPAGNE

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

https://ccbr.github.io/CHAMPAGNE/

MIT License

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Calculate fraction of reads in promoters & enhancer regions #82

Open kelly-sovacool opened 10 months ago

kelly-sovacool commented 10 months ago

Related to #30

need GTF file

can we keep info about each promoter? remove ones with no reads. rather than just summarize across all promoters. could then extract genes with high promoter activity, make clusters.

kopardev commented 8 months ago

getting promoters -> https://github.com/CCBR/ASPEN/blob/master/resources/frip/create_promoters_bed.py

kopardev commented 8 months ago

promoters and enhancers are already precalculated here --> https://github.com/CCBR/ASPEN/tree/master/resources/frip