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")
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
UnMapped Mapped Duplicates MapQPass
0 29479443 26274707 21742611