I have ATAC sequencing data for two types of cells, each with three replicates. Get strange results by DiffBind analysis. Why is my volcano map only halfway？ I don't know where I went wrong. Is there a problem with the original data or with the processing results? Can anyone answer it. here is my SampleSheet.
last.BAM was compared to the genome.Mitochondrial duplication, PCR duplication and low-quality reads were removed. Paired-ended sequencing to the same chromosome
here is my code
a <- dba(sampleSheet="diff.csv") a <- dba.count(a,bUseSummarizeOverlaps = TRUE) #warning:In serialize(data, node$con) : #'package:stats' may not be available when loading dba.plotPCA(a,attributes=DBA_FACTOR,label=DBA_ID) #figure2 plot(a) #figure3 a <- dba.contrast(a,categories = DBA_FACTOR,minMembers = 2) a <- dba.analyze(a,method=DBA_DESEQ2) #warning: solve(): system is singular (rcond: 3.89123e-18); attempting approx solution dba.show(a,bContrasts = T) # Factor Group Samples Group2 Samples2 DB.DESeq2 # 1 Factor ab 3 aa 3 8 dba.plotMA(a) #warning:In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin, :Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' #figure4 #This picture is weird. dba.plotVolcano(a) #figure5 sessionInfo( )