diff --git a/Tuesday/GREAT/GREAT_analysis_forEpigenomicData.md b/Tuesday/GREAT/GREAT_analysis_forEpigenomicData.md index 036e6cc67a395208922b01d2811e823698541aa3..a52b8c05afba7c08dafebc7ff2099d855578a932 100644 --- a/Tuesday/GREAT/GREAT_analysis_forEpigenomicData.md +++ b/Tuesday/GREAT/GREAT_analysis_forEpigenomicData.md @@ -10,7 +10,7 @@ ChIP-seq for SUMO2 in synchronized WI-38 fibroblasts at four different cell cycl <details> <summary markdown="span">What's the actual input data for the functional analyis?</summary> -Input data for functional analysis are regions (peaks) showing significant changes in SUMO enrichment among cell cycle (CC) phases, classified in 4 profiles by profile clustering. +Input data for functional analysis are regions (peaks, bed files) showing significant changes in SUMO enrichment among cell cycle (CC) phases, classified in 4 profiles by profile clustering. ChIPseq analyis done using hg19. </details> @@ -21,9 +21,7 @@ ChIPseq analyis done using hg19. * Go to http://great.stanford.edu/public/html/ -* Choose test and backgroung regions - -<details> +* Choose test and backgroung regions <details> <summary markdown="span">How how you chose the background regions?</summary> Depends on your question: Do you want to compare the functional enrichment in comparison to any random region of the region (Whole genome) or, else, in comparison to a given subset of regions that may have a specific genomic context (e.g. all the SUMO peaks that change along the CC).