Hello everyone, I have some question in building samplesheet:

1. When I am using narrowPeak files for my peaks, what is the difference between filling in "bed" and "narrow" in the "PeakCaller" column?
2. If my peak files are in the broadPeak format, how should I fill in the "PeakCaller" column for these files?

And I used the following code for analysis,

< samples <- dba(sampleSheet = "XX.csv", minOverlap = 2)

< samples SampleID Condition Replicate bamReads Peaks PeakCaller vec-1 vec 1 a1.bam a1.broadPeak bed vec-2 vec 2 a2.bam a2.broadPeak bed oe-1 oe 1 a1.bam a1.broadPeak bed oe-2 oe 2 a2.bam a2.broadPeak bed

< rm_blacklist <- dba.blacklist(samples, blacklist = DBA_BLACKLIST_MM10, greylist = F)

< blacklisted <- dba.blacklist(rm_blacklist, Retrieve = DBA_BLACKLISTED_PEAKS)

< count <- dba.count(rm_blacklist, summits=F, minOverlap = 2, bUseSummarizeOverlaps=TRUE)

< norm_count <- dba.normalize(count)

< contrast_count <- dba.contrast(norm_count, contrast=c("Condition", "vec", "oe"), minMembers = 2)

analysis_count <- dba.analyze(contrast_count, method=DBA_DESEQ2),

The analysis results show that I obtained 146 peaks with changes, Loss : 139, Gain: 7, and I use

profiles <- dba.plotProfile(analysis_count) dba.plotProfile(profiles)

But there are only vec have Loss lines in the Profile , no Gain lines, and the oe have no lines in Profile,

Could you please help me to solve these questions, thank you very much!