diffRepsOutput

Explanation of the diffReps' columns

Column Name	Explanation
Chrom	Chromosome name
Start	1-based start coordinate
End	1-based end coordinate (inclusive)
Length	Length of the differential site in bps
Treatment.cnt	Normalized read counts of the treatment group (separated by semi-colon)
Control.cnt	Normalized read counts of the control group (separated by semi-colon)
Treatment.avg	Avg. count (normalized) of the treatment group
Control.avg	Avg. count (normalized) of the control group
Treatment.enr	Fold enrichment vs. input based on avg. count (normalized) for treatment group
Control.enr	Fold enrichment vs. input based on avg. count (normalized) for control group
Event	Direction of enrichment change using the control group as reference
log2FC	Log2 fold change
pval	P-value
padj	BH-adjusted p-value (FDR)
winSta	Start coordinate of the core window which is the window with most significant p-value among the site
winEnd	End coordinate of the core window
winFC	Log2 fold change of the core window
winP	P-value of the core window
winQ	Adjusted p-value of the core window
GName	Associated gene name
TName	Associated transcript name
Strand	Associated transcription strand
TSS	Associated transcript start site
TES	Associated transcript end site
Feature	Classification of the site's location
D2TSS	Distance from the site center to the associated transcript's TSS

Column Name	Explanation
Chrom	Chromosome name
Start	1-based start coordinate
End	1-based end coordinate (inclusive)
Length	Length of the hotspot in bps
enrich	Enrichment ratio (compared with background)
pval	P-value of enrichment
padj	Adjusted p-value
nsite	Number of differential sites in the hotspot
Sites	One-string description of the hotspots. The differential sites are separated by semi-colon. Each differential site is described by filename:(info columns separated by comma):line_number.
ntype	Number of different types of chromatin marks in the hotspot
MarkType	Unique chromatin marks in the hotspot. In order for findHotspots to recognize mark names, you must make the diffReps output file names contain "standard" chromatin mark names. Such as, diffout.h3k4me3.txt, diffout.h3k9ac.txt, diffout.polII.txt. If it cannot recognize the marks, it will put the whole file names here.