Hi,

I apologize if I missed this question somewhere.

I am new to the ChIPQC package. When I put my bam file into the ChIPQC, it always gives me unmapped read =0. I know this is not the case as the bam file is simply generated by samtools sort. If I feed this bam file to samtools idxstats, it will give certain number of unmapped reads. 

I tried this in single sample in ChIPQCsample(bam, peak) as well as in group in ChIPQC(experiment,annotation="hg19", chromosomes = NULL) but the unmapped read is always 0. Is there anything I did wrong? Thank you!

test = ChIPQCsample("bam/LW-L1_S1_L004.marked.bam", peaks="macs2/LW-L1_S1_L004_peaks.broadPeak")
QCmetrics(test)
flagtagcounts(test)

> QCmetrics(test)
       Reads         Map%        Filt%         Dup%        ReadL        FragL 
29479443.000      100.000       26.200       87.100       50.000      105.000 
       RelCC          SSD         RiP% 
      -0.104        5.520       16.800 
> flagtagcounts(test)
         UnMapped            Mapped        Duplicates          MapQPass 
                0          29479443          26274707          21742611 
   MapQPassAndDup DuplicateByChIPQC 
         18946647            320941