Entering edit mode
paddiee18
•
0
@paddiee18-22738
Last seen 4.3 years ago
Hi,
I am trying to find the consensus regions between samples using narrow peak files that I generated using MACS2 for differential analysis for ATAC-seq. I am using runConsensusRegions but i am getting an empty list back.
peaks <- dir("~/Desktop/atac/ATAC/data/macs2/", pattern = "*.narrowPeak", full.names = TRUE)
myPeaks <- lapply (peaks, ChIPQC:::GetGRanges, simple = TRUE)
names(myPeaks) <- c("pairedEndPeakSample1_peaks", "pairedEndPeakSample2_peaks", "pairedEndPeakSample3_peaks", "pairedEndPeakSample4_peaks", "pairedEndPeakSample5_peaks", "pairedEndPeakSample6_peaks")
Group <- factor(c("WT", "KO", "WT", "KO", "WT", "KO"))
consensusToCount <- soGGi:::runConsensusRegions(GRangesList(myPeaks), "none")
consensusToCount has no value...
Hello! For creating a consensus peak file, I did it through the command line, rather than through R, if you're interested in that route.
Additionally adding to this thread, I am also having a related problem in that when I have the consensus peak files, I can't annotate them to get a GTF/GFF file to be used as a "reference genome" for differential analysis.